An atlas of substrate specificities for the human serine/threonine kinome

Highly accurate protein structure prediction with AlphaFold

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works

The protein kinase complement of the human genome

Manning, G., Whyte, D. B., Martinez, R., Hunter, T., & Sudarsanam, S. (2002) · Science · doi:10.1126/science.1075762 · Cited by 8,145 · see citing works

Accurate prediction of protein structures and interactions using a 3-track network

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,542 · see citing works

Mitogen-Activated Protein Kinase Pathways Mediated by ERK, JNK, and p38 Protein Kinases

Johnson, G. L., & Lapadat, R. (2002) · Science · doi:10.1126/science.1072682 · Cited by 4,295 · see citing works

Oncogenic kinase signalling.

Blume-Jensen, P., & Hunter, T. (2001) · Nature · doi:10.1038/35077225 · Cited by 3,738 · see citing works

Mass-spectrometric exploration of proteome structure and function

Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334 · see citing works

CREB: A Stimulus-Induced Transcription Factor Activated by A Diverse Array of Extracellular Signals

Shaywitz, A. J., & Greenberg, M. E. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.821 · Cited by 2,135 · see citing works

GSK-3: tricks of the trade for a multi-tasking kinase

Doble, B. W., & Woodgett, J. R. (2003) · Journal of Cell Science · doi:10.1242/jcs.00384 · Cited by 2,084 · see citing works

Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs

Obenauer, J. C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg584 · Cited by 1,602 · see citing works

The renaissance of GSK3

Cohen, P., & Frame, S. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35096075 · Cited by 1,478 · see citing works

Mechanisms of specificity in protein phosphorylation

Ubersax, J. A., & Ferrell Jr, J. E. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2203 · Cited by 1,451 · see citing works

An Adenosine 3′,5′-Monophosphate-dependant Protein Kinase from Rabbit Skeletal Muscle

Walsh, D. A., Perkins, J. P., & Krebs, E. G. (1968) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)34204-8 · Cited by 1,448 · see citing works

One‐thousand‐and‐one substrates of protein kinase CK2?

Meggio, F., & Pinna, L. A. (2003) · The FASEB Journal · doi:10.1096/fj.02-0473rev · Cited by 1,315 · see citing works

The nuts and bolts of AGC protein kinases

Pearce, L. R., Komander, D., & Alessi, D. R. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2822 · Cited by 1,294 · see citing works

The origins of protein phosphorylation

Cohen, P. (2002) · Nature Cell Biology · doi:10.1038/ncb0502-e127 · Cited by 1,147 · see citing works

Protein kinase recognition sequence motifs

Kemp, B. E., & Pearson, R. B. (1990) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(90)90073-k · Cited by 1,010 · see citing works

Kinase inhibitors: the road ahead

Ferguson, F. M., & Gray, N. S. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2018.21 · Cited by 1,009 · see citing works

Regulation of p53 in response to DNA damage

Lakin, N. D., & Jackson, S. P. (1999) · Oncogene · doi:10.1038/sj.onc.1203015 · Cited by 987 · see citing works

Protein kinases: evolution of dynamic regulatory proteins

Taylor, S. S., & Kornev, A. P. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.09.006 · Cited by 940 · see citing works

ggseqlogo: a versatile R package for drawing sequence logos

Wagih, O. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx469 · Cited by 933 · see citing works

THE RELATION OF ADENOSINE-3', 5'-PHOSPHATE AND PHOSPHORYLASE TO THE ACTIONS OF CATECHOLAMINES AND OTHER HORMONES

Sutherland, E. W., & Rall, T. W. (1960) · Pharmacological Reviews · doi:10.1016/s0031-6997(25)06975-3 · Cited by 913 · see citing works

Quantitative Analysis of Hsp90-Client Interactions Reveals Principles of Substrate Recognition

Taipale, M., Krykbaeva, I., Koeva, M., Kayatekin, C., Westover, K. D., Karras, G. I., & Lindquist, S. (2012) · Cell · doi:10.1016/j.cell.2012.06.047 · Cited by 879 · see citing works

Role of multiple basic residues in determining the substrate specificity of cyclic AMP-dependent protein kinase.

Kemp, B. E., Graves, D. J., Benjamini, E., & Krebs, E. G. (1977) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)40137-2 · Cited by 835 · see citing works

Substrate Specificities and Identification of Putative Substrates of ATM Kinase Family Members

Kim, S.-T., Lim, D.-S., Canman, C. E., & Kastan, M. B. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.53.37538 · Cited by 810 · see citing works

Systematic Discovery of In Vivo Phosphorylation Networks

Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A. T. M., Jørgensen, C., Miron, I. M., Diella, F., Colwill, K., Taylor, L., Elder, K., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.052 · Cited by 735 · see citing works

Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery

Macůrek, L., Lindqvist, A., Lim, D., Lampson, M. A., Klompmaker, R., Freire, R., Clouin, C., Taylor, S. S., Yaffe, M. B., & Medema, R. H. (2008) · Nature · doi:10.1038/nature07185 · Cited by 710 · see citing works

The biological impact of mass-spectrometry-based proteomics

Cravatt, B. F., Simon, G. M., & Yates, J. R. (2007) · Nature · doi:10.1038/nature06525 · Cited by 705 · see citing works

GRKs and β-arrestins: roles in receptor silencing, trafficking and signaling

Reiter, É., & Lefkowitz, R. J. (2006) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2006.03.008 · Cited by 680 · see citing works

Regulation of Receptor Trafficking by GRKs and Arrestins

Moore, C. A. C., Milano, S. K., & Benovic, J. (2006) · Annual Review of Physiology · doi:10.1146/annurev.physiol.69.022405.154712 · Cited by 677 · see citing works

α-KETO ACID DEHYDROGENASE COMPLEXES, X. REGULATION OF THE ACTIVITY OF THE PYRUVATE DEHYDROGENASE COMPLEX FROM BEEF KIDNEY MITOCHONDRIA BY PHOSPHORYLATION AND DEPHOSPHORYLATION

Linn, T. C., Pettit, F. H., & Reed, L. J. (1969) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.62.1.234 · Cited by 671 · see citing works

Use of an oriented peptide library to determine the optimal substrates of protein kinases

Songyang, Z., Blechner, S., Hoagland, N., Hoekstra, M. F., Piwnica-Worms, H. M., & Cantley, L. C. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00221-9 · Cited by 654 · see citing works

Signalling ballet in space and time

Kholodenko, B. Ν., Hancock, J. F., & Kölch, W. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2901 · Cited by 618 · see citing works

p53-Deficient Cells Rely on ATM- and ATR-Mediated Checkpoint Signaling through the p38MAPK/MK2 Pathway for Survival after DNA Damage

Reinhardt, H. C., Aslanian, A., Lees, J. A., & Yaffe, M. B. (2007) · Cancer Cell · doi:10.1016/j.ccr.2006.11.024 · Cited by 593 · see citing works

What turns CREB on?

Johannessen, M., Delghandi, M. P., & Moens, U. L. (2004) · Cellular Signalling · doi:10.1016/j.cellsig.2004.05.001 · Cited by 592 · see citing works

Mixed-lineage kinase control of JNK and p38 MAPK pathways

Gallo, K. A., & Johnson, G. L. (2002) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm906 · Cited by 572 · see citing works

Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells

Kettenbach, A. N., Schweppe, D. K., Faherty, B. K., Pechenick, D. A., Pletnev, A. A., & Gerber, S. A. (2011) · Science Signaling · doi:10.1126/scisignal.2001497 · Cited by 531 · see citing works

MAP4K family kinases act in parallel to MST1/2 to activate LATS1/2 in the Hippo pathway

Meng, Z., Moroishi, T., Mottier, V., Plouffe, S. W., Hansen, C. G., Hong, A. W., Park, H. W., Mo, J., Lü, W., Lu, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms9357 · Cited by 524 · see citing works

A motif-based profile scanning approach for genome-wide prediction of signaling pathways

Yaffe, M. B., Leparc, G. G., Lai, J., Obata, T., Volinia, S., & Cantley, L. C. (2001) · Nature Biotechnology · doi:10.1038/86737 · Cited by 517 · see citing works

Cyclin-dependent kinases: a family portrait

Malumbres, M., Harlow, E. E., Hunt, T., Hunter, T. R., Lahti, J. M., Manning, G., Morgan, D. O., Tsai, L., & Wolgemuth, D. J. (2009) · Nature Cell Biology · doi:10.1038/ncb1109-1275 · Cited by 499 · see citing works

Kinases that control the cell cycle in response to DNA damage: Chk1, Chk2, and MK2

Reinhardt, H. C., & Yaffe, M. B. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.01.018 · Cited by 494 · see citing works

The functional landscape of the human phosphoproteome

Ochoa, D., Jarnuczak, A. F., Viéitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A. A., Hill, A., Garcia-Alonso, L., Stein, F., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0344-3 · Cited by 491 · see citing works

How do protein kinases recognize their substrates?

Pinna, L. A., & Ruzzene, M. (1996) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/s0167-4889(96)00083-3 · Cited by 471 · see citing works

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

Eick, D., & Geyer, M. (2013) · Chemical Reviews · doi:10.1021/cr400071f · Cited by 470 · see citing works

Small-molecule kinase inhibitors: an analysis of FDA-approved drugs

Wu, P., Nielsen, T. E., & Clausen, M. H. (2016) · Drug Discovery Today · doi:10.1016/j.drudis.2015.07.008 · Cited by 457 · see citing works

Linear Motif Atlas for Phosphorylation-Dependent Signaling

Miller, M. L., Jensen, L. J., Diella, F., Jørgensen, C., Tinti, M., Li, L., Hsiung, M. S., Parker, S. A., Bordeaux, J., Sicheritz‐Pontén, T., et al. (2008) · Science Signaling · doi:10.1126/scisignal.1159433 · Cited by 439 · see citing works

The Structural Basis for Control of Eukaryotic Protein Kinases

Endicott, J., Noble, M. E. M., & Johnson, L. N. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-052410-090317 · Cited by 431 · see citing works

Why nature chose phosphate to modify proteins

Hunter, T. R. (2012) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0013 · Cited by 430 · see citing works

Kinase mutations in human disease: interpreting genotype–phenotype relationships

Lahiry, P., Torkamani, A., Schork, N. J., & Hegele, R. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2707 · Cited by 420 · see citing works

Too many roads not taken

Edwards, A. M., Isserlin, R., Bader, G. D., Frye, S. V., Willson, T. M., & Yu, F. H. (2011) · Nature · doi:10.1038/470163a · Cited by 411 · see citing works

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

Humphrey, S. J., Yang, G., Yang, P., Fazakerley, D. J., Stöckli, J., Yang, J. Y. H., & James, D. E. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.04.010 · Cited by 411 · see citing works

Definition of a consensus sequence for peptide substrate recognition by p44mpk, the meiosis-activated myelin basic protein kinase

Clark‐Lewis, I., Sanghera, J. S., & Pelech, S. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)98601-1 · Cited by 406 · see citing works

A rapid method for determining protein kinase phosphorylation specificity

Hutti, J. E., Jarrell, E. T., Chang, J. D., Abbott, D. W., Störz, P., Toker, A., Cantley, L. C., & Turk, B. E. (2004) · Nature Methods · doi:10.1038/nmeth708 · Cited by 356 · see citing works

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms

Hornbeck, P. V., Kornhauser, J. M., Latham, V. M., Murray, B., Nandhikonda, V., Nord, A., Skrzypek, E., Wheeler, T. J., Zhang, B., & Gnad, F. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1159 · Cited by 348 · see citing works

Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs

Mok, J., Kim, P. M., Lam, H. Y. K., Piccirillo, S., Zhou, X., Jeschke, G. R., Sheridan, D. L., Parker, S. A., Desai, V., Jwa, M., et al. (2010) · Science Signaling · doi:10.1126/scisignal.2000482 · Cited by 343 · see citing works

A Single Kinase Generates the Majority of the Secreted Phosphoproteome

Tagliabracci, V. S., Wiley, S. E., Guo, X. Q., Kinch, L. N., Durrant, E. S., Wen, J., Xiao, J., Cui, J., Nguyen, K. B., Engel, J. D., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.028 · Cited by 338 · see citing works

Phosphate groups as substrate determinants for casein kinase I action.

Flotow, H., Graves, P. R., Wang, A. Q., Fiol, C. J., Roeske, R. W., & Roach, P. J. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)77295-5 · Cited by 337 · see citing works

Illuminating the dark phosphoproteome

Needham, E. J., Parker, B. L., Burykin, T., James, D. E., & Humphrey, S. J. (2019) · Science Signaling · doi:10.1126/scisignal.aau8645 · Cited by 322 · see citing works

Intrinsically disordered proteins drive membrane curvature

Busch, D. J., Houser, J. R., Hayden, C. C., Sherman, M. B., Lafer, E. M., & Stachowiak, J. C. (2015) · Nature Communications · doi:10.1038/ncomms8875 · Cited by 278 · see citing works

Alpha-kinase 1 is a cytosolic innate immune receptor for bacterial ADP-heptose

Zhou, P., She, Y., Dong, N., Li, P., He, H., Borio, A., Wu, Q., Lu, S., Ding, X., Cao, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0433-3 · Cited by 270 · see citing works

Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

Riley, N. M., & Coon, J. J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04123 · Cited by 265 · see citing works

A Mitotic Phosphorylation Feedback Network Connects Cdk1, Plk1, 53BP1, and Chk2 to Inactivate the G2/M DNA Damage Checkpoint

van Vugt, M. A. T. M., Gardino, A. K., Linding, R., Ostheimer, G. J., Reinhardt, H. C., Ong, S.-E., Tan, C. S. H., Miao, H., Keezer, S. M., Li, J., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000287 · Cited by 228 · see citing works

Plk3 Functionally Links DNA Damage to Cell Cycle Arrest and Apoptosis at Least in Part via the p53 Pathway

Xie, S., Wu, H., Wang, Q., Cogswell, J. P., Husain, I., Conn, C. W., Stambrook, P. J., Jhanwar‐Uniyal, M., & Dai, W. H. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m106050200 · Cited by 226 · see citing works

Homing in: Mechanisms of Substrate Targeting by Protein Kinases

Miller, C. J., & Turk, B. E. (2018) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2018.02.009 · Cited by 201 · see citing works

Structure of the Site Phosphorylated in the Phosphorylase b to a Reaction

Fischer, E. H., Graves, D. J., Snyder, E. R., & Krebs, E. G. (1959) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)69910-7 · Cited by 196 · see citing works

Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition

Czudnochowski, N., Bösken, C. A., & Geyer, M. (2012) · Nature Communications · doi:10.1038/ncomms1846 · Cited by 191 · see citing works

Utilization of Oriented Peptide Libraries to Identify Substrate Motifs Selected by ATM

O'Neill, T., Dwyer, A. J., Ziv, Y., Chan, D. W., Lees-Miller, S. P., Abraham, R. H., Lai, J. H., Hill, D., Shiloh, Y., Cantley, L. C., et al. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m001002200 · Cited by 189 · see citing works

Site specificity of casein kinase‐2 (TS) from rat liver cytosol

Marin, O., Meggio, F., Marchiori, F., Borin, G., & Pinna, L. A. (1986) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1986.tb09962.x · Cited by 188 · see citing works

MELK is not necessary for the proliferation of basal-like breast cancer cells

Huang, H., Seo, H., Zhang, T., Wang, Y., Jiang, B., Li, Q., Buckley, D. L., Nabet, B., Roberts, J. M., Paulk, J., et al. (2017) · eLife · doi:10.7554/elife.26693 · Cited by 178 · see citing works

Spatial Exclusivity Combined with Positive and Negative Selection of Phosphorylation Motifs Is the Basis for Context-Dependent Mitotic Signaling

Alexander, J., Lim, D., Joughin, B. A., Hegemann, B., Hutchins, J. R. A., Ehrenberger, T., Ivins, F. J., Sessa, F., Hudecz, O., Nigg, E. A., et al. (2011) · Science Signaling · doi:10.1126/scisignal.2001796 · Cited by 174 · see citing works

The phosphoproteomics data explosion

Lemeer, S., & Heck, A. J. R. (2009) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2009.06.022 · Cited by 173 · see citing works

A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains

Modi, V., & Dunbrack, R. L. (2019) · Scientific Reports · doi:10.1038/s41598-019-56499-4 · Cited by 171 · see citing works

pHisphorylation: the emergence of histidine phosphorylation as a reversible regulatory modification

Fuhs, S. R., & Hunter, T. R. (2017) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.12.010 · Cited by 166 · see citing works

Crystal structure of a BRAF kinase domain monomer explains basis for allosteric regulation

Thevakumaran, N., Lavoie, H., Critton, D., Tebben, A. J., Marinier, A., Sicheri, F., & Therrien, M. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2924 · Cited by 162 · see citing works

Ordered multisite protein phosphorylation. Analysis of glycogen synthase kinase 3 action using model peptide substrates.

Fiol, C. J., Wang, A. Q., Roeske, R. W., & Roach, P. J. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)39291-9 · Cited by 158 · see citing works

Structural and functional analysis of the Cdk13/Cyclin K complex

Greifenberg, A. K., Hönig, D., Pilarova, K., Düster, R., Bartholomeeusen, K., Bösken, C. A., Anand, K., Blazek, D., & Geyer, M. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.025 · Cited by 157 · see citing works

Structure Guided Design of Potent and Selective Ponatinib-Based Hybrid Inhibitors for RIPK1

Najjar, M., Suebsuwong, C., Ray, S. S., Thapa, R. J., Maki, J. L., Nogusa, S., Shah, S., Saleh, D., Gough, P. J., Bertin, J., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.052 · Cited by 153 · see citing works

The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases

Berginski, M. E., Moret, N., Liu, C., Goldfarb, D., Sorger, P. K., & Gomez, S. M. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa853 · Cited by 148 · see citing works

MO25 is a master regulator of SPAK/OSR1 and MST3/MST4/YSK1 protein kinases

Filippi, B., Heros, P. D. L., Mehellou, Y., Navratilova, I. H., Gourlay, R., Deák, M., Plater, L., Toth, R. L., Zeqiraj, E., & Alessi, D. R. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.78 · Cited by 144 · see citing works

Secreted protein kinases

Tagliabracci, V. S., Pinna, L. A., & Dixon, J. E. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.11.008 · Cited by 125 · see citing works

The N-terminal ERK-binding Site of MEK1 Is Required for Efficient Feedback Phosphorylation by ERK2 in Vitro and ERK Activation in Vivo

Xu, B.-E., Wilsbacher, J. L., Collisson, T., & Cobb, M. H. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.48.34029 · Cited by 109 · see citing works

Discovery of a selective inhibitor of doublecortin like kinase 1

Ferguson, F. M., Nabet, B., Raghavan, S., Liu, Y., Leggett, A. L., Kuljanin, M., Kalekar, R. L., Yang, A., He, S., Wang, J., et al. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0506-0 · Cited by 109 · see citing works

Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity

Chen, C., Ha, B. H., Thévenin, A. F., Lou, H. J., Zhang, R., Yip, K. Y.-L., Peterson, J. R., Gerstein, M., Kim, P. M., Filippakopoulos, P., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2013.11.013 · Cited by 102 · see citing works

An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor

Shah, N. H., Wang, Q., Yan, Q., Karandur, D., Kadlecek, T. A., Fallahee, I., Russ, W. P., Ranganathan, R., Weiss, A., & Kuriyan, J. (2016) · eLife · doi:10.7554/elife.20105 · Cited by 96 · see citing works

Structures of SMG1-UPFs Complexes: SMG1 Contributes to Regulate UPF2-Dependent Activation of UPF1 in NMD

Melero, R., Uchiyama, A., Castaño, R., Kataoka, N., Kurosawa, H., Ohno, S., Yamashita, A., & Llorca, Ó. (2014) · Structure · doi:10.1016/j.str.2014.05.015 · Cited by 91 · see citing works

Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Yaron, T. M., Heaton, B. E., Levy, T. M., Johnson, J. L., Jordan, T. X., Cohen, B. M., Kerelsky, A., Lin, T.-Y., Liberatore, K. M., Bulaon, D. K., et al. (2022) · Science Signaling · doi:10.1126/scisignal.abm0808 · Cited by 91 · see citing works

Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcriptionPreprint

Rimel, J. K., Poss, Z. C., Erickson, B., Maas, Z. L., Ebmeier, C. C., Johnson, J. L., Decker, T.-M., Yaron, T. M., Bradley, M. J., Hamman, K. B., et al. (2020) · Genes & Development · doi:10.1101/gad.341545.120 · Cited by 87 · see citing works

Unmasking Determinants of Specificity in the Human Kinome

Creixell, P., Palmeri, A., Miller, C. J., Lou, H. J., Santini, C. C., Nielsen, M., Turk, B. E., & Linding, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.057 · Cited by 85 · see citing works

Chaperonins groEL and groES promote assembly of heterotetramers (alpha 2 beta 2) of mammalian mitochondrial branched-chain alpha-keto acid decarboxylase in Escherichia coli.

Wynn, R., Davie, J., Cox, R. P., & Chuang, D. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)42286-7 · Cited by 78 · see citing works

A precisely positioned MED12 activation helix stimulates CDK8 kinase activity

Klatt, F., Leitner, A., Kim, I. V., Ho-Xuan, H., Schneider, E. V., Langhammer, F., Weinmann, R., Müller, M., Huber, R., Meister, G., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1917635117 · Cited by 75 · see citing works

Crystal structure of the catalytic domain of Haspin, an atypical kinase implicated in chromatin organization

Villa, F., Capasso, P., Tortorici, M., Forneris, F., de Marco, A., Mattevi, A., & Musacchio, A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908485106 · Cited by 69 · see citing works

Macrophages employ quorum licensing to regulate collective activation

Muldoon, J. J., Chuang, Y., Bagheri, N., & Leonard, J. N. (2020) · Nature Communications · doi:10.1038/s41467-020-14547-y · Cited by 68 · see citing works

Identification of amphiphysin 1 as an endogenous substrate for CDKL5, a protein kinase associated with X-linked neurodevelopmental disorder

Sekiguchi, M., Katayama, S., Hatano, N., Shigeri, Y., Sueyoshi, N., & Kameshita, I. (2013) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2013.04.012 · Cited by 68 · see citing works

Exceptional Disfavor for Proline at the P+1 Position among AGC and CAMK Kinases Establishes Reciprocal Specificity between Them and the Proline-directed Kinases

Zhu, G., Fujii, K., Belkina, N., Liu, Y., James, M. N. G., Herrero, J. J., & Shaw, S. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m413159200 · Cited by 64 · see citing works

Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7

Wan, L. C. K., Maisonneuve, P., Szilard, R. K., Lambert, J., Ng, T. F., Manczyk, N., Huang, H., Laister, R. C., Caudy, A. A., Gingras, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1181 · Cited by 64 · see citing works

Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen

Shah, N. H., Löbel, M., Weiss, A., & Kuriyan, J. (2018) · eLife · doi:10.7554/elife.35190 · Cited by 63 · see citing works

Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1)

Balasuriya, N., Davey, N. E., Johnson, J. L., Liu, H., Biggar, K. K., Cantley, L. C., Li, S. S. ‐., & O’Donoghue, P. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.012425 · Cited by 63 · see citing works

Amino acid sequence of the phosphorylated site in rabbit liver glycogen phosphorylase

Wolf, D. P., Fischer, E. H., & Krebs, E. G. (1970) · Biochemistry · doi:10.1021/bi00811a010 · Cited by 61 · see citing works

Quantitative phosphoproteomics to characterize signaling networks

Rigbolt, K. T. G., & Blagoev, B. (2012) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2012.05.006 · Cited by 60 · see citing works

hSMG-1 and ATM sequentially and independently regulate the G1 checkpoint during oxidative stress

Gehen, S. C., Staversky, R. J., Bambara, R. A., Keng, P. C., & O’Reilly, M. A. (2008) · Oncogene · doi:10.1038/onc.2008.48 · Cited by 57 · see citing works

Physiological Processes Modulated by the Chloride-Sensitive WNK-SPAK/OSR1 Kinase Signaling Pathway and the Cation-Coupled Chloride Cotransporters

Murillo‐de‐Ozores, A. R., Chávez‐Canales, M., Heros, P. D. L., Gamba, G., & Castañeda‐Bueno, M. (2020) · Frontiers in Physiology · doi:10.3389/fphys.2020.585907 · Cited by 55 · see citing works

Major phosphorylation of SF1 on adjacent Ser‐Pro motifs enhances interaction with U2AF65

Manceau, V., Swenson, M. C., Caër, J. L., Sobel, A., Kielkopf, C. L., & Maucuer, A. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2005.05091.x · Cited by 53 · see citing works

The FDA-approved drug Alectinib compromises SARS-CoV-2 nucleocapsid phosphorylation and inhibits viral infection in vitroPreprint

Yaron, T. M., Heaton, B. E., Levy, T. M., Johnson, J. L., Jordan, T. X., Cohen, B. M., Kerelsky, A., Lin, T.-Y., Liberatore, K. M., Bulaon, D. K., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.14.251207 · Cited by 51 · see citing works

An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression

Albanese, S. K., Parton, D. L., Işık, M., Rodríguez‐Laureano, L., Hanson, S. M., Behr, J. M., Gradia, S., Jeans, C., Levinson, N. M., Seeliger, M. A., et al. (2018) · Biochemistry · doi:10.1021/acs.biochem.7b01081 · Cited by 48 · see citing works

Substrate profiling of human vaccinia-related kinases identifies coilin, a Cajal body nuclear protein, as a phosphorylation target with neurological implications

Sanz-García, M., Vázquez-Cedeira, M., Kellerman, E., Renbaum, P., Levy‐Lahad, E., & Lazo, P. A. (2011) · Journal of Proteomics · doi:10.1016/j.jprot.2011.08.019 · Cited by 47 · see citing works

SnapShot: Clinical proteomics

Zhu, Y., Aebersold, R. H., Mann, M., & Guo, T. (2021) · Cell · doi:10.1016/j.cell.2021.08.015 · Cited by 43 · see citing works

STK25 suppresses Hippo signaling by regulating SAV1-STRIPAK antagonism

Bae, S. J., Ni, L., & Luo, X. (2020) · eLife · doi:10.7554/elife.54863 · Cited by 41 · see citing works

Mitochondrial DNA damage as a potential biomarker of LRRK2 kinase activity in LRRK2 Parkinson’s disease

González-Hunt, C. P., Thacker, E., Toste, C. M., Boularand, S., Deprets, S., Dubois, L., & Sanders, L. H. (2020) · Scientific Reports · doi:10.1038/s41598-020-74195-6 · Cited by 40 · see citing works

Regulation of folate and methionine metabolism by multisite phosphorylation of human methylenetetrahydrofolate reductase

Zheng, Y., Ramsamooj, S., Li, Q., Johnson, J. L., Yaron, T. M., Sharra, K., & Cantley, L. C. (2019) · Scientific Reports · doi:10.1038/s41598-019-40950-7 · Cited by 39 · see citing works

Phosphoproteomics of Acute Cell Stressors Targeting Exercise Signaling Networks Reveal Drug Interactions Regulating Protein Secretion

Needham, E. J., Humphrey, S. J., Cooke, K. C., Fazakerley, D. J., Duan, X., Parker, B. L., & James, D. E. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.001 · Cited by 33 · see citing works

Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity

Ferguson, F. M., Doctor, Z. M., Ficarro, S. B., Browne, C. M., Marto, J. A., Johnson, J. L., Yaron, T. M., Cantley, L. C., Kim, N. D., Sim, T., et al. (2019) · Cell chemical biology · doi:10.1016/j.chembiol.2019.02.015 · Cited by 32 · see citing works

A resource for exploring the understudied human kinome for research and therapeutic opportunitiesPreprint

Moret, N., Liu, C., Gyori, B. M., Bachman, J. A., Steppi, A., Hug, C. B., Taujale, R., Huang, L., Berginski, M. E., Gomez, S. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.02.022277 · Cited by 32 · see citing works

Deciphering the Acute Cellular Phosphoproteome Response to Irradiation with X-rays, Protons and Carbon Ions

Winter, M., Đokić, I., Schlegel, J., Warnken, U. H., Debus, J., Abdollahi, A., & Schnölzer, M. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.066597 · Cited by 32 · see citing works

Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases

Bradley, D. T. C., Viéitez, C., Rajeeve, V., Selkrig, J., Cutillas, P. R., & Beltrão, P. (2021) · Cell Reports · doi:10.1016/j.celrep.2020.108602 · Cited by 29 · see citing works

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling

Mertins, P., Przybylski, D., Yosef, N., Qiao, J., Clauser, K. R., Raychowdhury, R., Eisenhaure, T., Maritzen, T., Haucke, V., Satoh, T., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.016 · Cited by 28 · see citing works

Development of a CDK10/CycM in vitro Kinase Screening Assay and Identification of First Small-Molecule Inhibitors

Robert, T., Johnson, J. L., Guichaoua, R., Yaron, T. M., Bach, S., Cantley, L. C., & Colas, P. (2020) · Frontiers in Chemistry · doi:10.3389/fchem.2020.00147 · Cited by 28 · see citing works

Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing

Liu, Y., Ferguson, F. M., Li, L., Kuljanin, M., Mills, C. E., Subramanian, K., Harshbarger, W. D., Gondi, S. R., Wang, J., Sorger, P. K., et al. (2020) · Cell chemical biology · doi:10.1016/j.chembiol.2020.07.011 · Cited by 21 · see citing works

Encapsulation of an 86-kDa Assembly Intermediate inside the Cavities of GroEL and Its Single-ring Variant SR1 by GroES

Song, J., Li­, ­., Huang, Y., & Chuang, D. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m209705200 · Cited by 15 · see citing works

Mutation of Serine 1333 in the ATR HEAT Repeats Creates a Hyperactive Kinase

Luzwick, J. W., Nam, E. A., Zhao, R., & Cortez, D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099397 · Cited by 14 · see citing works

Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks

Joughin, B. A., Liu, C., Lauffenburger, D. A., Hogue, C. W. V., & Yaffe, M. B. (2012) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0010 · Cited by 12 · see citing works

Enrichr-KG: bridging enrichment analysis across multiple libraries

Evangelista, J. E., Xie, Z., Marino, G. B., Nguyen, N. L. U., Clarke, D. J. B., & Ma’ayan, A. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad393 · Cited by 233 · see citing works

Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Geffen, Y., Anand, S. K., Akiyama, Y., Yaron, T. M., Song, Y., Johnson, J. L., Govindan, A., Babur, Ö., Li, Y., Huntsman, E. M., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.013 · Cited by 210 · see citing works

ELM—the Eukaryotic Linear Motif resource—2024 update

Kumar, M., Michael, S., Alvarado-Valverde, J., Zeke, A., Lázár, T., Glavina, J., Nagy‐Kanta, E., Donagh, J. M., Kálmán, Z. E., Pascarelli, S., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1058 · Cited by 185 · see citing works

Multi-pass, single-molecule nanopore reading of long protein strands

Motone, K., Kontogiorgos-Heintz, D., Wee, J., Kurihara, K., Yang, S., Roote, G., Fox, O., Fang, Y., Queen, M., Tolhurst, M., et al. (2024) · Nature · doi:10.1038/s41586-024-07935-7 · Cited by 155 · see citing works

The intrinsic substrate specificity of the human tyrosine kinome

Yaron, T. M., Joughin, B. A., Huntsman, E. M., Kerelsky, A., Cizin, D. M., Cohen, B. M., Regev, A., Song, J., Vasan, N., Lin, T.-Y., et al. (2024) · Nature · doi:10.1038/s41586-024-07407-y · Cited by 151 · see citing works

Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst

Hsiao, Y., Zhang, H., Li, G. X., Deng, Y., Yu, F., Kahrood, H. V., Steele, J. R., Schittenhelm, R. B., & Nesvizhskii, A. I. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00294 · Cited by 152 · see citing works

Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources

Diamant, I., Clarke, D. J. B., Evangelista, J. E., Lingam, N., & Ma’ayan, A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1080 · Cited by 149 · see citing works

The Cyclin-dependent kinase 1: more than a cell cycle regulator

Massacci, G., Perfetto, L., & Sacco, F. (2023) · British Journal of Cancer · doi:10.1038/s41416-023-02468-8 · Cited by 141 · see citing works

The ribotoxic stress response drives UV-mediated cell death

Sinha, N. K., McKenney, C. D., Yeow, Z. Y., Li, J. J., Nam, K. H., Yaron, T. M., Johnson, J. L., Huntsman, E. M., Cantley, L. C., Ordureau, A., et al. (2024) · Cell · doi:10.1016/j.cell.2024.05.018 · Cited by 142 · see citing works

Navigating the ERK1/2 MAPK Cascade

Martín-Vega, A., & Cobb, M. H. (2023) · Biomolecules · doi:10.3390/biom13101555 · Cited by 124 · see citing works

Pan-cancer proteogenomics connects oncogenic drivers to functional states

Li, Y., Porta‐Pardo, E., Tokheim, C. J., Bailey, M. H., Yaron, T. M., Stathias, V., Geffen, Y., Imbach, K. J., Cao, S., Anand, S. K., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.014 · Cited by 114 · see citing works

RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer

Jbara, A., Lin, K., Stossel, C., Siegfried, Z., Shqerat, H., Amar-Schwartz, A., Elyada, E., Mogilevsky, M., Raitses‐Gurevich, M., Johnson, J. L., et al. (2023) · Nature · doi:10.1038/s41586-023-05820-3 · Cited by 96 · see citing works

Pan-cancer proteogenomics characterization of tumor immunity

Petralia, F., Ma, W., Yaron, T. M., Caruso, F. P., Tignor, N. L., Wang, J. M., Charytonowicz, D., Johnson, J. L., Huntsman, E. M., Marino, G. B., et al. (2024) · Cell · doi:10.1016/j.cell.2024.01.027 · Cited by 96 · see citing works

A neurodegenerative cellular stress response linked to dark microglia and toxic lipid secretion

Flury, A. G., Aljayousi, L., Park, H.-J., Khakpour, M., Mechler, J., Aziz, S., McGrath, J. D., Deme, P., Sandberg, C., Ibáñez, F. G., et al. (2024) · Neuron · doi:10.1016/j.neuron.2024.11.018 · Cited by 98 · see citing works

Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors

Reinecke, M., Brear, P., Vornholz, L., Berger, B., Seefried, F., Wilhelm, S., Samaras, P., Gyenis, L., Litchfield, D. W., Médard, G., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-023-01459-3 · Cited by 94 · see citing works

The logic of protein post‐translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments

Suskiewicz, M. (2024) · Bioessays · doi:10.1002/bies.202300178 · Cited by 84 · see citing works

Instrumentation at the leading edge of proteomics

Peters-Clarke, T. M., Coon, J., & Riley, N. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04497 · Cited by 78 · see citing works

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

(2024) · doi:10.1038/s41467-024-51274-0 · Cited by 83 · see citing works

Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer

Klomp, J. E., Diehl, J. N., Klomp, J. A., Edwards, A. C., Yang, R., Morales, A. J., Taylor, K. E., Drizyte-Miller, K., Bryant, K. L., Schaefer, A., et al. (2024) · Science · doi:10.1126/science.adk0850 · Cited by 83 · see citing works

Micronuclear collapse from oxidative damage

Bona, M. D., Chen, Y., Agustinus, A. S., Mazzagatti, A., Paez, M. A. D., Deyell, M., Bronder, D., Hickling, J. H., Hong, C., Scipioni, L., et al. (2024) · Science · doi:10.1126/science.adj8691 · Cited by 82 · see citing works

A critical evaluation of protein kinase regulation by activation loop autophosphorylation

Reinhardt, R., & Leonard, T. A. (2023) · eLife · doi:10.7554/elife.88210 · Cited by 76 · see citing works

Leucine-Rich Repeat Kinases

Alessi, D. R., & Pfeffer, S. R. (2024) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-030122-051144 · Cited by 70 · see citing works

Multi-scale signaling and tumor evolution in high-grade gliomas

Liu, J., Cao, S., Imbach, K. J., Gritsenko, M. A., Lih, T. M., Kyle, J. E., Yaron-Barir, T. M., Binder, Z. A., Li, Y., Strunilin, I., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2024.06.004 · Cited by 69 · see citing works

Multi-omics characterization of the monkeypox virus infection

Huang, Y., Bergant, V., Grass, V., Emslander, Q., Hamad, M. S., Hubel, P., Mergner, J., Piras, A., Krey, K., Henrici, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51074-6 · Cited by 68 · see citing works

Targeted protein posttranslational modifications by chemically induced proximity for cancer therapy

Peng, Y., Liu, J., Inuzuka, H., & Wei, W. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104572 · Cited by 66 · see citing works

The metabolic sensor AMPK: Twelve enzymes in one

Smiles, W. J., Ovens, A. J., Oakhill, J. S., & Kofler, B. (2024) · Molecular Metabolism · doi:10.1016/j.molmet.2024.102042 · Cited by 65 · see citing works

Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism

Frei, M. S., Mehta, S., & Zhang, J. (2024) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-030722-021359 · Cited by 64 · see citing works

Distinct states of nucleolar stress induced by anticancer drugs

Potapova, T., Unruh, J. R., Conkright-Fincham, J., Banks, C. A. S., Florens, L. A., Schneider, D. A., & Gerton, J. L. (2023) · eLife · doi:10.7554/elife.88799 · Cited by 55 · see citing works

Comparative Efficacy and Selectivity of Pharmacological Inhibitors of DYRK and CLK Protein Kinases

Lindberg, M. F., Deau, E., Arfwedson, J., George, N. S., George, P. G., Alfonso, P., Corrionero, A., & Meijer, L. (2023) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c02068 · Cited by 52 · see citing works

AMPK targets PDZD8 to trigger carbon source shift from glucose to glutamine

Li, M., Wang, Y., Wei, X., Cai, W.-F., Wu, J., Zhu, M., Wang, Y., Liu, Y., Xiong, J., Qu, Q., et al. (2024) · Cell Research · doi:10.1038/s41422-024-00985-6 · Cited by 52 · see citing works

Altered translation elongation contributes to key hallmarks of aging in the killifish brain

Fraia, D. D., Marino, A., Lee, J. H., Sacramento, E. K., Baumgart, M., Bagnoli, S., Balla, T., Schalk, F., Kamrad, S., Guan, R., et al. (2025) · Science · doi:10.1126/science.adk3079 · Cited by 55 · see citing works

Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor

Darabedian, N., Ji, W., Fan, M., Lin, S., Seo, H., Vinogradova, E. V., Yaron, T. M., Mills, E. L., Xiao, H., Senkane, K., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-023-01273-x · Cited by 51 · see citing works

GLP-1R signaling neighborhoods associate with the susceptibility to adverse drug reactions of incretin mimetics

Wright, S. C., Motso, A., Koutsilieri, S., Beusch, C. M., Sabatier, P., Berghella, A., Blondel-Tepaz, É., Mangenot, K., Pittarokoilis, I., Sismanoglou, D.-C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41893-4 · Cited by 47 · see citing works

The AMPK Pathway: Molecular Rejuvenation of Metabolism and Mitochondria

Malik, N., & Shaw, R. J. (2025) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-094431 · Cited by 52 · see citing works

A global phosphosite-correlated network map of Thousand And One Kinase 1 (TAOK1)

Priyanka, P., Gopalakrishnan, A. P., Nisar, M., Shivamurthy, P. B., George, M., John, L., Sanjeev, D., Yandigeri, T., Thomas, S. D., Rafi, A., et al. (2024) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2024.106558 · Cited by 45 · see citing works

An RNA damage response network mediates the lethality of 5-FU in colorectal cancer

Chen, J.-K., Merrick, K. A., Kong, Y. W., Izrael-Tomasevic, A., Eng, G. M., Handly, E. D., Patterson, J. C., Cannell, I. G., Suárez-López, L., Hosios, A. M., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101778 · Cited by 44 · see citing works

Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions

Li, W., Dasgupta, A., Yang, K., Wang, S., Kumar, N. H., Chepyala, S. R., Yarbro, J. M., Hu, Z., Šalovská, B., Fornasiero, E. F., et al. (2025) · Cell · doi:10.1016/j.cell.2025.02.021 · Cited by 47 · see citing works

Pancreatic cancer: molecular pathogenesis and emerging therapeutic strategies

Rozengurt, E., & Eibl, G. (2026) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-025-02499-y · Cited by 45 · see citing works

Personalized molecular signatures of insulin resistance and type 2 diabetes

Kjærgaard, J., Stocks, B., Henderson, J., Freemantle, J. B., Rizo‐Roca, D., Puglia, M., Montoya, M. M., Andersson, D. P., Bäckdahl, J., Hogling, D. E., et al. (2025) · Cell · doi:10.1016/j.cell.2025.05.005 · Cited by 43 · see citing works

An Update on Protein Kinases as Therapeutic Targets—Part I: Protein Kinase C Activation and Its Role in Cancer and Cardiovascular Diseases

Silnitsky, S., Rubin, S. J. S., Zerihun, M., & Qvit, N. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242417600 · Cited by 42 · see citing works

Redefining metalloproteases specificity through network proteolysis

Kollet, Ó., Das, A., Karamanos, N. K., Keller, U. A. D., & Sagi, I. (2023) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2023.11.001 · Cited by 40 · see citing works

Orchestrating Intracellular Calcium Signaling Cascades by Phosphosite-Centric Regulatory Network: A Comprehensive Analysis on Kinases CAMKK1 and CAMKK2

Mahin, A., Gopalakrishnan, A. P., Ahmed, M., Nisar, M., John, L., Shivamurthy, P. B., Ummar, S., Varghese, S., Modi, P. K., Pai, V. R., et al. (2025) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2024.0196 · Cited by 38 · see citing works

CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves

Bayer, F. P., Gander, M., Küster, B., & The, M. (2023) · Nature Communications · doi:10.1038/s41467-023-43696-z · Cited by 37 · see citing works

Phosphorylation of PFKL regulates metabolic reprogramming in macrophages following pattern recognition receptor activation

Wang, M., Flaswinkel, H., Joshi, A., Napoli, M., Masgrau‐Alsina, S., Kamper, J. M., Henne, A., Heinz, A., Bérouti, M., Schmacke, N. A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50104-7 · Cited by 37 · see citing works

TOR complex 2 is a master regulator of plasma membrane homeostasis

Thorner, J. W. (2022) · Biochemical Journal · doi:10.1042/bcj20220388 · Cited by 36 · see citing works

Substrate and phosphorylation site selection by phosphoprotein phosphatases

Nguyen, H. T., & Kettenbach, A. N. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.04.004 · Cited by 36 · see citing works

Food perception promotes phosphorylation of MFFS131 and mitochondrial fragmentation in liver

Henschke, S., Nolte, H., Magoley, J., Kleele, T., Brandt, C., Hausen, A. C., Wunderlich, C. M., Bauder, C. A., Aschauer, P., Manley, S., et al. (2024) · Science · doi:10.1126/science.adk1005 · Cited by 35 · see citing works

P-stalk ribosomes act as master regulators of cytokine-mediated processes

Dopler, A., Alkan, F., Malka, Y., van der Kammen, R., Hoefakker, K., Taranto, D., Kocabay, N., Mimpen, I. L., Ramirez, C. F. A., Malzer, E., et al. (2024) · Cell · doi:10.1016/j.cell.2024.09.039 · Cited by 35 · see citing works

Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions

Zhou, Z., Yeung, W., Gravel, N., Salcedo, M. V., Soleymani, S., Li, S., & Kannan, N. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad046 · Cited by 34 · see citing works

The molecular basis of cell memory in mammals: The epigenetic cycle

Espinosa-Martínez, M., Alcázar‐Fabra, M., & Landeira, D. (2024) · Science Advances · doi:10.1126/sciadv.adl3188 · Cited by 33 · see citing works

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions

Rrustemi, T., Meyer, K., Roske, Y., Uyar, B., Akalin, A., Imami, K., Ishihama, Y., Daumke, O., & Selbach, M. (2024) · Nature Communications · doi:10.1038/s41467-024-46794-8 · Cited by 32 · see citing works

Targeting ALDH1A1 to enhance the efficacy of KRAS-targeted therapy through ferroptosis

Bian, Y., Shan, G., Bi, G., Liang, J., Hu, Z., Sui, Q., Shi, H., Zheng, Z., Yao, G., Wang, Q., et al. (2024) · Redox Biology · doi:10.1016/j.redox.2024.103361 · Cited by 34 · see citing works

Personalized phosphoproteomics of skeletal muscle insulin resistance and exercise links MINDY1 to insulin action

Needham, E. J., Hingst, J. R., Onslev, J., Díaz‐Vegas, A., Leandersson, M. R., Huckstep, H., Kristensen, J. M., Kido, K., Richter, E. A., Højlund, K., et al. (2024) · Cell Metabolism · doi:10.1016/j.cmet.2024.10.020 · Cited by 34 · see citing works

Unraveling the Mystery of Insulin Resistance: From Principle Mechanistic Insights and Consequences to Therapeutic Interventions

Mir, R., Jeelani, M., Alharthi, M. H., Rizvi, S. F., Sohail, S. K., Wani, J. I., Sabah, Z. U., BinAfif, W. F., Nandi, P. S., Alshahrani, A. M., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26062770 · Cited by 40 · see citing works

The insulin signalling network

Burchfield, J. G., Díaz‐Vegas, A., & James, D. E. (2025) · Nature Metabolism · doi:10.1038/s42255-025-01349-z · Cited by 34 · see citing works

FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma

Zhen, Y., Liu, K., Shi, L., Shah, S., Xu, Q., Ellis, H., Balasooriya, E. R., Kreuzer, J., Morris, R. T., Baldwin, A. S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47514-y · Cited by 33 · see citing works

µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics

Oliinyk, D., Will, A., Schneidmadel, F. R., Böhme, M., Rinke, J., Hochhaus, A., Ernst, T., Hahn, N., Geis, C., Lubeck, M., et al. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00050-9 · Cited by 37 · see citing works

SARS-CoV-2 hijacks p38β/MAPK11 to promote virus replication

Higgins, C. A., Nilsson-Payant, B. E., Kurland, A. P., Ye, C., Ярон, Т., Johnson, J. L., Bonaventure, B., Adhikary, P., Golynker, I., Panis, M., et al. (2023) · mBio · doi:10.1128/mbio.01007-23 · Cited by 33 · see citing works

Integrative proteogenomic profiling of high-risk prostate cancer samples from Chinese patients indicates metabolic vulnerabilities and diagnostic biomarkers

Dong, B., Xu, J., Huang, Y., Guo, J., Dong, Q., Wang, Y., Li, N., Liu, Q., Zhang, M., Pan‐Hammarström, Q., et al. (2024) · Nature Cancer · doi:10.1038/s43018-024-00820-2 · Cited by 31 · see citing works

High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display

Li, A., Voleti, R., Lee, M., Gagoski, D., & Shah, N. H. (2023) · eLife · doi:10.7554/elife.82345 · Cited by 31 · see citing works

Structural insights into the activation of ataxia-telangiectasia mutated by oxidative stress

Howes, A. C., Perišić, O., & Williams, R. L. (2023) · Science Advances · doi:10.1126/sciadv.adi8291 · Cited by 31 · see citing works

GPCR kinases differentially modulate biased signaling downstream of CXCR3 depending on their subcellular localization

Gardner, J., Eiger, D. S., Hicks, C., Choi, I., Pham, U., Chundi, A., Namjoshi, O. A., & Rajagopal, S. (2024) · Science Signaling · doi:10.1126/scisignal.add9139 · Cited by 30 · see citing works

Comprehensive evaluation of phosphoproteomic-based kinase activity inference

Müller‐Dott, S., Jaehnig, E. J., Munchic, K. P., Jiang, W., Yaron, T. M., Savage, S. R., Garrido‐Rodríguez, M., Johnson, J. L., Lussana, A., Petsalaki, E., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59779-y · Cited by 32 · see citing works

ROS-induced cytosolic release of mitochondrial PGAM5 promotes colorectal cancer progression by interacting with MST3

Wang, S., Wu, X., Bi, W., Xu, J., Hou, L., Li, G., Pan, Y., Zhang, H., Li, M., Du, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56444-2 · Cited by 29 · see citing works

CSNK2 suppresses autophagy by activating FLN-NHL-containing TRIM proteins

Hoenigsperger, H., Koepke, L., Acharya, D., Hunszinger, V., Freisem, D., Grenzner, A., Wiese, S., Kirchhoff, F., Gack, M. U., & Sparrer, K. M. J. (2023) · Autophagy · doi:10.1080/15548627.2023.2281128 · Cited by 28 · see citing works

The expanding landscape of canonical and non-canonical protein phosphorylation

Houlès, T., Yoon, S.-O., & Roux, P. P. (2024) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2024.08.004 · Cited by 28 · see citing works

Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions

Kliche, J., Garvanska, D. H., Simonetti, L., Badgujar, D. C., Dobritzsch, D., Nilsson, J., Davey, N. E., & Ivarsson, Y. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211164 · Cited by 27 · see citing works

Molecular docking and dynamics in protein serine/threonine kinase drug discovery: advances, challenges, and future perspectives

Hasan, G. M., Mohammad, T., Zaidi, S., Shamsi, A., & Hassan, M. I. (2025) · Frontiers in Pharmacology · doi:10.3389/fphar.2025.1696204 · Cited by 27 · see citing works

An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells

Zhou, W., Li, W., Wang, S., Šalovská, B., Hu, Z., Tao, B., Di, Y., Punyamurtula, U., Turk, B. E., Sessa, W. C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39514-1 · Cited by 28 · see citing works

ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition

Borenäs, M., Umapathy, G., Lind, D. E., Lai, W., Guan, J., Johansson, J., Jennische, E., Schmidt, A., Kurhe, Y., Gabre, J. L., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2315242121 · Cited by 26 · see citing works

Tyr352 as a Predominant Phosphosite in the Understudied Kinase and Molecular Target, HIPK1: Implications for Cancer Therapy

Sanjeev, D., George, M., John, L., Gopalakrishnan, A. P., Priyanka, P., Mendon, S., Yandigeri, T., Nisar, M., Nisar, M., Kanekar, S., et al. (2024) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2023.0244 · Cited by 26 · see citing works

Substrate recognition principles for the PP2A-B55 protein phosphatase

Kruse, T., Garvanska, D. H., Varga, J. K., Garland, W., McEwan, B. C., Hein, J. B., Weisser, M. B., Benavides-Puy, I., Chan, C. B., Sotelo-Parrilla, P., et al. (2024) · Science Advances · doi:10.1126/sciadv.adp5491 · Cited by 26 · see citing works

Structural basis of Cdk7 activation by dual T-loop phosphorylation

Düster, R., Anand, K., Binder, S. C., Schmitz, M., Gatterdam, K., Fisher, R. P., & Geyer, M. (2024) · Nature Communications · doi:10.1038/s41467-024-50891-z · Cited by 26 · see citing works

Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput

Kennedy, P. H., Sheikh, A. A. D., Balakar, M., Jones, A. C., Olive, M. E., Hegde, M., Matias, M. I., Pirete, N., Burt, R. A., Levy, J. M., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02256-z · Cited by 29 · see citing works

A Rapid One-Pot Workflow for Sensitive Microscale Phosphoproteomics

Muneer, G., Chen, C., Lee, T. D., Chen, B., & Chen, Y. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00862 · Cited by 25 · see citing works

Neutrophils with low production of reactive oxygen species are activated during immune priming and promote development of arthritis

Chen, T., Zhou, Z., Liu, Y., Xu, J., Zhu, C., Sun, R., Hu, H., Liu, Y., Dai, L., Holmdahl, R., et al. (2024) · Redox Biology · doi:10.1016/j.redox.2024.103401 · Cited by 26 · see citing works

CD24 is a promising immunotherapeutic target for enhancing efficacy of third‐generation EGFR‐TKIs on EGFR‐mutated lung cancer

Liang, J., Bi, G., Huang, X., Xu, Z., Huang, Y., Bian, Y., Shan, G., Guo, W., Yan, Y., Sui, Q., et al. (2025) · 癌症：英文版 · doi:10.1002/cac2.70068 · Cited by 25 · see citing works

Significance of RB Loss in Unlocking Phenotypic Plasticity in Advanced Cancers

Venkadakrishnan, V. B., Yamada, Y., Weng, K., Idahor, O., & Beltran, H. (2023) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-23-0045 · Cited by 27 · see citing works

High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma

Arang, N., Lubrano, S., Ceribelli, M., Rigiracciolo, D. C., Saddawi‐Konefka, R., Faraji, F., Ramirez, S. I., Kim, D., Tosto, F. A., Stevenson, E. J., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101244 · Cited by 26 · see citing works

Phosphoproteomic Analysis of CARMIL1 Reveals Novel Regulatory Mechanisms and Upstream Kinases Involved in Actin Dynamics and Cell Migration

Sheela, A., Mahin, A., Ummar, S., Vattoth, N. N., Dcunha, L., Gopalakrishnan, A. P., & Raju, R. (2025) · Cytoskeleton · doi:10.1002/cm.70001 · Cited by 24 · see citing works

The choreography of protein kinase PDK1 and its diverse substrate dance partners

Leroux, A. E., & Biondi, R. M. (2023) · Biochemical Journal · doi:10.1042/bcj20220396 · Cited by 24 · see citing works

Phosphorylation of DNA-binding domains of CLOCK–BMAL1 complex for PER-dependent inhibition in circadian clock of mammalian cells

Otobe, Y., Jeong, E. M., Ito, S., Shinohara, Y., Kurabayashi, N., Aiba, A., Fukada, Y., Kim, J. K., & Yoshitane, H. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2316858121 · Cited by 23 · see citing works

Unravelling the phosphoregulatory network of protein kinase C-delta (PKC-δ)

Raghu, D. H., Dcunha, L., Ahmed, M., Fahma, A., Mahin, A., Gopalakrishnan, A. P., John, L., Subair, S., Shivamurthy, P. B., Varghese, S., et al. (2025) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2025.141080 · Cited by 23 · see citing works

Principles of phosphoproteomics and applications in cancer research

Higgins, L., Gerdes, H., & Cutillas, P. (2023) · Biochemical Journal · doi:10.1042/bcj20220220 · Cited by 19 · see citing works

CK1δ/ε kinases regulate TDP-43 phosphorylation and are therapeutic targets for ALS-related TDP-43 hyperphosphorylation

Ko, V. I., Ong, K., Cleveland, D. W., Yu, H., & Ravits, J. (2024) · Neurobiology of Disease · doi:10.1016/j.nbd.2024.106516 · Cited by 22 · see citing works

The prospect of substrate-based kinase inhibitors to improve target selectivity and overcome drug resistance

Biswas, B., Huang, Y., Craik, D. J., & Wang, C. K. L. (2024) · Chemical Science · doi:10.1039/d4sc01088d · Cited by 23 · see citing works

The Rho guanine dissociation inhibitor α inhibits skeletal muscle Rac1 activity and insulin action

Møller, L. L. V., Ali, M. S., Davey, J. R., Raun, S. H., Andersen, N. R., Long, J. Z., Qian, H., Jeppesen, J. F., Henríquez‐Olguín, C., Frank, E., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2211041120 · Cited by 22 · see citing works

Targeted degradation of CDK9 potently disrupts the MYC-regulated network

Toure, M. A., Motoyama, K., Xiang, Y., Urgiles, J., Kabinger, F., Koglin, A.-S., Iyer, R. S., Gagnon, K., Kumar, A., Ojeda, S., et al. (2025) · Cell chemical biology · doi:10.1016/j.chembiol.2025.03.001 · Cited by 22 · see citing works

Genetic Encoding of Phosphorylated Amino Acids into Proteins

Allen, M., Karplus, P. A., Mehl, R. A., & Cooley, R. B. (2024) · Chemical Reviews · doi:10.1021/acs.chemrev.4c00110 · Cited by 21 · see citing works

Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification

Hein, J. B., Nguyen, H. T., Garvanska, D. H., Nasa, I., Kruse, T., Feng, Y., Mendez, B. L., Davey, N. E., Kettenbach, A. N., Fordyce, P. M., et al. (2023) · Molecular Systems Biology · doi:10.15252/msb.202311782 · Cited by 20 · see citing works

Aberrant cytoplasmic expression of UHRF1 restrains the MHC-I-mediated anti-tumor immune response

Tan, L., Yin, T., Xiang, H., Wang, L., Mudgal, P., Chen, J., Ding, Y., Wang, G., Lim, B. J. W., Huang, Y., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52902-5 · Cited by 20 · see citing works

Metabolic mapping of the human solute carrier superfamily

Wiedmer, T., Teoh, S. T., Christodoulaki, E., Wolf, G., Tian, C., Sedlyarov, V., Jarret, A. P., Leippe, P., Frommelt, F., Inglés‐Prieto, Á., et al. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00106-4 · Cited by 21 · see citing works

DYRK1A signalling synchronizes the mitochondrial import pathways for metabolic rewiring

Marada, A., Walter, C., Suhm, T., Shankar, S., Nandy, A., Brummer, T., Dhaouadi, I., Vögtle, F. ‐., & Meisinger, C. (2024) · Nature Communications · doi:10.1038/s41467-024-49611-4 · Cited by 19 · see citing works

CDK signaling via nonconventional CDK phosphorylation sites

Valk, E., Örd, M., Faustova, I., & Loog, M. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-06-0196 · Cited by 19 · see citing works

Illuminating function of the understudied druggable kinome

Gomez, S. M., Axtman, A. D., Willson, T. M., Major, M. B., Townsend, R., Sorger, P. K., & Johnson, G. L. (2024) · Drug Discovery Today · doi:10.1016/j.drudis.2024.103881 · Cited by 19 · see citing works

Aging-related alterations in mechanistic target of rapamycin signaling promote platelet hyperreactivity and thrombosis

Portier, I., Manne, B. K., Kosaka, Y., Tolley, N. D., Denorme, F., Babur, Ö., Reddy, A. P., Wilmarth, P. A., Aslan, J. E., Weyrich, A. S., et al. (2024) · Journal of Thrombosis and Haemostasis · doi:10.1016/j.jtha.2024.05.025 · Cited by 19 · see citing works

Protein kinase A and local signaling in cancer

Rosenthal, K. J., Gordan, J. D., & Scott, J. D. (2024) · Biochemical Journal · doi:10.1042/bcj20230352 · Cited by 18 · see citing works

Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites

Jiang, W., Jaehnig, E. J., Liao, Y., Shi, Z., Yaron, T. M., Johnson, J. L., Cantley, L. C., & Zhang, B. (2025) · Nature Communications · doi:10.1038/s41467-025-57993-2 · Cited by 20 · see citing works

Comprehensive PTM profiling with SCASP-PTM uncovers mechanisms of p62 degradation and ALDOA-mediated tumor progression

Lin, Z.-P., Gan, G., Xu, X., Wen, C., Ding, X., Chen, X., Zhang, K., Guo, W., Lin, M., Wang, Y.-Y., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115500 · Cited by 18 · see citing works

Deciphering the functional landscape of phosphosites with deep neural network

Liang, Z. T., Liu, T., Li, Q., Zhang, G., Zhang, B., Du, X.-K., Liu, J., Chen, Z., Ding, H., Hu, G., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113048 · Cited by 19 · see citing works

The Kinase Library: a Global Atlas of the Human Protein Kinome and Its Applications From Cancer to Covid-19

Yaron, T. M. (2022) · eCommons (Cornell University)

Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library

Barber, K. W., Miller, C. J., Jun, J. W., Lou, H. J., Turk, B. E., & Rinehart, J. (2018) · Biochemistry · doi:10.1021/acs.biochem.8b00410 · Cited by 15 · see citing works

Large-scale Discovery of Substrates of the Human Kinome

Sugiyama, N., Imamura, H., & Ishihama, Y. (2019) · Scientific Reports · doi:10.1038/s41598-019-46385-4 · Cited by 121 · see citing works

Abstract 3487: An atlas of substrate specificities for the human tyrosine kinome

Johnson, J. L., Yaron, T. M., Cantley, L. C., Yaffe, M. B., Turk, B. E., Huntsman, E. M., & Hornbeck, P. V. (2023) · Cancer Research · doi:10.1158/1538-7445.am2023-3487

Systematic identification and quantification of substrate specificity determinants in human protein kinases = Identificación y cuantificación sistemática de determinantes de la especificidad por sustrato en las proteínas quinasas de humano

Tarajano, A., & Alejandro, M. (2013) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)