Publications

Here are recent publications from the Center, both in our research and collaborative capacities:

2009

Scheeff, ED, Eswaran, J, Bunkoczi, G, Knapp, S, Manning, G. Structure of the pseudokinase VRK3 reveals a degraded catalytic site, a highly conserved kinase fold, and a putative regulatory binding site. Structure 17:128-38 (PDF, Medline, Perspective, Website).

Copp, J, Manning, G, Hunter, T. TORC specific phosphorylation of mTOR: phospho-Ser2481 is a marker for intact mTORC2. Cancer Research 69:1821-7 (Medline, PDF).

Bomati, EK, Manning, G, Deheyn, DD. Amphioxus encodes the largest known family of green fluorescent proteins, which have diversified into distinct functional classes. BMC Evol. Biol. 9: 77 (Medline, PDF).

Scheeff, ED and Fink, JL. Fundamentals of Protein Structure. In Structural Bioinformatics, 2nd ed. (ed. Gu, J and Bourne PE) Wiley-Blackwell, Ch 2:15-40 (Website).

Manning, G, Hunter, T. Eukaryotic Kinomes: Genomics and Evolution of Protein Kinases. In Handbook of Cell Signaling, 2nd ed. (ed. Bradshaw, RA and Dennis, E). Academic Press, San Diego (Amazon).

Zhang, Y-W, Brognard, J, Coughlin, C, You, Z, Dolled-Filhart, M, Aslanian, A, Manning, G, Abraham, RT, Hunter, T. The F Box Protein Fbx6 Regulates Chk1 Stability and Cellular Sensitivity to Replication Stress. Molecular Cell, 35:442-453 (Medline, PDF).

Malumbres, M, Harlow, E, Hunt, T, Hunter, T, Lahti, JM, Manning, G, Morgan, DO, Tsai, L-H, Wolgemuth, DJ. Cyclin-dependent kinases: a family portrait. Nature Cell Biology, 11:1275-6 (Medline, PDF).

Nathanson, JL, Jappelli, R, Scheeff, E, Manning, G, Yanagawa, Y, Obata, K, Brenner, S, Callaway, EM. Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but Do Not Restrict Activity to Specific Inhibitory Cell-Types. Frontiers in Neural Circuits, 3:19 (Medline, PDF).

Hutt, DM, Herman, D, Rodrigues, APC, Noel, S, Pilewski, J, Matteson, J, Kellner, W, Kelly, JW, de Jonge, HR, Riordan, JR, Sorscher, E, Frizzell, RA, Manning, G, Gottesfeld, JM, Balch, WE. Epigenomic Correction of Cystic Fibrosis through HDAC Modification. Nature Chemical Biology, 6:25-33 (Medline, PDF).

Scheeff, ED, Axelrod, HL, Miller, MD, Chiu, H-J, Deacon, AM, Wilson, IA, Manning, G. Genomics, Evolution and Crystal Structure of a New Family of Bacterial Spore Kinases. Proteins in press (PDF).

2008

King, N, Westbrook, MJ, Young, SL, Kuo, A, Abedin, M, Chapman, J, Fairclough, S, Hellsten, U, Isogai, Y, Letunic, I, Marr, M, Pincus, D, Putman, N, Rokas, A, Wright, KJ, Zuzow, R, Dirks, W, Good, M, Goodstein, D, Lemons, D, Li, W, Lyos, J, Morris, A, Nichols, S, Richter, DJ, Salamov, A, JGI Sequencing, Bork, P, Lim, WA, Manning, G, Miller, WT, McGinnis, W, Shapiro, H, Tijan, R, Grigoriev, IV, Rokhsar, D. The genome of the choanoflagellate Monosiga brevicollis and the origins of metazoan multicellularity. Nature 451, 783-788 (Medline, PDF)

Manning, G, Young, SL, Miller, WT, Zhai, Y. The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan. PNAS, 105: 9674-79 (PDF, Medline, website).
      Science's Editor's Choice, and a 2008 Signaling Breakthrough of the Year by Science Signaling.

Vilar, M, Chou, H-T, Luhrs, T, Maji, S, Riek-Loher, D, Verel, R, Manning, G, Stahlberg, H, Riek, R. The Fold of α-Synuclein Fibrils. PNAS 105:8637-42 (Medline, PDF).

O'Maille, PE, Malone, A, Dellas, N, Hess, A, Sheehan, I, Greenhagen, B, Chappell, J, Manning, G, Noel, JP. Phylogenetically and structurally defined sequence space connecting divergent plant sesquiterpene synthases. Nature Chemical Biology, 4:617-23 (Medline, PDF).

2007

Natarajan, K, Taylor, S, Zhai, Y, Venter, C, Manning, G. Structure and function of the microbial kinome. PLoS Biol. 5(3):e17. (Medline, PDF)

Yooseph, S., G. Sutton, D.B. Rusch, S. Williamson, A.L. Halpern, K. Remington, J.A. Eisen, K. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. Miller, H. Li, S.T. Mashiyama, M. Joachimiak, C.v. Belle, J.-M. Chandonia, D. Soergel, Y. Zhai, K. Natarajan, S. Lee, B.J. Raphael, V. Bafna, R. Friedman, S.E. Brenner, A. Godzik, D. Eisenberg, J. Dixon, S. Taylor, M. Frazier, R. Strausberg and J.C. Venter. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol. 5(3):e16 (Medline, PDF)

Morrison, HG, McArthur, AG, Gillin, FD, Aley, SB, Adam, RD, Olsen, GJ, Reiner, DS, Svard, SG, Elmendorf, HG, Hehl, AB, Samuelson, J, Nixon, JEJ, Passamaneck, NE, Kim, UU, Lasek-Nesselquist, E, Cipriano, MJ, Holder, ME, Huse, SM, Palm, D, Best, AA, Reich, CI, Manning, G, Nigam, A, Prabu, A, Davids, BS, Sogin, ML. Genomic minimalism in the early diverging intestinal parasite, Giardia lamblia. Science 317(5846):1921-6 (Medline, PDF)

Chung JL, Beaver JE, Scheeff ED, Bourne PE. Con-Struct Map: a comparative contact map analysis tool. Bioinformatics 23:2491-2. (Medline, PDF)

Perrin. MH, Grace. CR, Digruccio. MR, Fischer. WH, Maji. SK, Cantle. JP, Smith S, Manning. G, Vale. WW, Riek. R. Distinct structural and functional roles of conserved residues in the first extracellular domain of receptors for corticotropin releasing factor and related G-protein coupled receptors. J. Biol. Chem. 282(52): 37529-36 (Medline, PDF)

Slabinski, L, Jaroszewski, L, Rodrigues, APC, Rychlewski, L, Wilson, IA, Lesley, SA, Godzik, A. The challenges of protein structure determination - lessons from structural genomics. Protein Science 16:2472-82 (Medline, PDF)

2006

Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314:941-52. (Medline, PDF)

Bradham, CA, Foltz, KR, Beane, WS, Arnone, MI, Rizzo, F, Coffman, JA, Mushegian, A, Goel, M, Morales, J, Geneviere, A, Lapraz, F, Robertson, AK, Kelkar, H, Loza-Coll, M, Townley, IK, Raisch, M, Rouz, MM, Legpage, T, Gache, C, McClay, DR, Manning, G. The Sea Urchin Kinome: A First Look. Dev. Biol. 300:180-93. (Medline, PDF)

Scheeff, ED, Bourne, PE. Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics 7:410 (Medline, PDF)

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, Del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Shotgun sequencing and analysis of the macronuclear genome of the model eukaryote, the ciliate Tetrahymena thermophila. PLoS Biol. 4 (9): e286. (Medline, PDF)

Schröfelbauer, B, Senger, T, Manning, G, Landau, NR. Alteration of HIV-1 Vif allows functional interaction with primate APOBEC3G. J. Virol. 80 (12), 5984-91. (Medline, PDF)

Wloga, D, Camba, A, Rogowski, K, Manning, G, Dziadosz, M, Gaertig, J. Members of the Nima-related Kinase family Promote Disassembly of Cilia by Multiple Mechanisms. Molec. Biol. Cell, 17(6): 2799-810. (Medline, PDF)

Goldberg, JM, Manning, G, Liu, A, Fey, P, Pilcher, KE, Xu, Y, Smith, JL. The Dictyostelium Kinome - Analysis of the Protein Kinases from a Simple Model Organism. PLoS Genet. 2 (3): e38 (Medline, PDF)

2005

Manning, G. Genomic overview of Protein Kinases (December 13, 2005), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.60.1, (HTML, PDF)

2004

Caenepeel, S, Charydczak, G, Sudarsanam, S. Hunter, T., Manning, G. The Mouse Kinome: Discovery and comparative genomics of all mouse protein kinases. PNAS 101 (32), 11707-12.(Medline, PDF)