Our Publications
Learn more about the work and impact of the Davis Lab
Kinetochore
- Flores RL, Peterson ZE, Zelter A, Riffle M, Asbury CL, Davis TN. Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load. J Cell Biol. 2022 May 2;221(5):e202107016.
- Ogren A, Parmar S, Mukherjee S, Gonzalez SJ, Plooster M, McClellan M, Mannava AG, Davidson E, Davis TN, Gardner MK. Kinesin-14 motors participate in a force balance at microtubule plus-ends to regulate dynamic instability. Proc Natl Acad Sci U S A. 2022 Feb 22;119(8):e2108046119.
- Laine LJ, Mäki-Jouppila JHE, Kutvonen E, Tiikkainen P, Nyholm TKM, Tien JF, Umbreit NT, Härmä V, Kallio L, Davis TN, Asbury CL, Poso A, Gorbsky GJ, Kallio MJ. VTT-006, an anti-mitotic compound, binds to the Ndc80 complex and suppresses cancer cell growth in vitro. Oncoscience. 2021 Dec 10;8:134-153.
- Hamilton GE, Davis TN. Biochemical evidence for diverse strategies in the inner kinetochore. Open Biol. 2020 Nov;10(11):200284.
- Gutierrez A, Kim JO, Umbreit NT, Asbury CL, Davis TN, Miller MP, Biggins S. Cdk1 Phosphorylation of the Dam1 Complex Strengthens Kinetochore-Microtubule Attachments. Curr Biol. 2020 Nov 16;30(22):4491-4499.e5.
- Miller MP, Evans RK, Zelter A, Geyer EA, MacCoss MJ, Rice LM, Davis TN, Asbury CL, Biggins S. Kinetochore-associated Stu2 promotes chromosome biorientation in vivo. PLoS Genet. 2019 Oct 4;15(10):e1008423.
- Hamilton GE, Helgeson LA, Noland CL, Asbury CL, Dimitrova YN, Davis TN. Reconstitution reveals two paths of force transmission through the kinetochore Elife. 2020;9:e56582.
- Scarborough EA, Davis TN, Asbury CL. Tight bending of the Ndc80 complex provides intrinsic regulation of its binding to microtubules. Elife 2019, 8.
- Helgeson LA, Zelter A, Riffle M, MacCoss MJ, Asbury CL, Davis TN. Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments. Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2740-2745.
- Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN. The Ndc80 complex bridges two Dam1 complex rings. Elife. 2017 Feb 13;6
- Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol. 2016 Jun;194(3):303-10.
- Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN. The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling. Nat Commun. 2015 Nov 12;6:8673.
- Kudalkar EM, Scarborough EA, Umbreit NT, Zelter A, Gestaut DR, Riffle M, Johnson RS, MacCoss MJ, Asbury CL, Davis TN. Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex. Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):E5583-9.
- Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR 3rd, MacCoss MJ, Moritz RL, Asbury CL, Davis TN. Kinetochore Biorientation in Saccharomyces cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex. Genetics. 2014 Dec;198(4):1483-93.
- Umbreit NT, Miller MP, Tien JF, Ortolá JC, Gui L, Lee KK, Biggins S, Asbury CL, Davis TN. Kinetochores require oligomerization of Dam1 complex to maintain microtubule attachments against tension and promote biorientation. Nat Commun. 2014 Sep 19;5:4951.
- Tien JF, Fong KK, Umbreit NT, Payen C, Zelter A, Asbury CL, Dunham MJ, Davis TN. Coupling unbiased mutagenesis to high-throughput DNA sequencing uncovers functional domains in the Ndc80 kinetochore protein of Saccharomyces cerevisiae. Genetics. 2013 Sep;195(1):159-70.
- Umbreit NT, Gestaut DR, Tien JF, Vollmar BS, Gonen T, Asbury CL, Davis TN. The Ndc80 kinetochore complex directly modulates microtubule dynamics. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16113-8.
- Graczyk B, Davis TN. An assay to measure the affinity of proteins for microtubules by quantitative fluorescent microscopy. Anal Biochem. 2011 Mar 15;410(2):313-5.
- Shimogawa MM, Wargacki MM, Muller EG, Davis TN. Laterally attached kinetochores recruit the checkpoint protein Bub1, but satisfy the spindle checkpoint. Cell Cycle. 2010 Sep;9(17):3619-28.
- Wargacki MM, Tay JC, Muller EG, Asbury CL, Davis TN. Kip3, the yeast kinesin-8, is required for clustering of kinetochores at metaphase. Cell Cycle. 2010 Jul;9(13):2579-86.
- Tien JF, Umbreit NT, Gestaut DR, Franck AD, Cooper J, Wordeman L, Gonen T, Asbury CL, Davis TN. Cooperation of the Dam1 and Ndc80 kinetochore complexes enhances microtubule coupling and is regulated by aurora B. J Cell Biol. 2010 May;189(4):713-23.
- Powers AF, Franck AD, Gestaut DR, Cooper J, Graczyk B, Wei RR, Wordeman L, Davis TN, Asbury CL. The Ndc80 kinetochore complex forms load-bearing attachments to dynamic microtubule tips via biased diffusion. Cell. 2009 Mar;136(5):865-75.
- Shimogawa MM, Widlund PO, Riffle M, Ess M, Davis TN. Bir1 is required for the tension checkpoint. Mol Biol Cell. 2009 Feb;20(3):915-23.
- Gestaut DR, Graczyk B, Cooper J, Widlund PO, Zelter A, Wordeman L, Asbury CL, Davis TN. Phosphoregulation and depolymerization-driven movement of the Dam1 complex do not require ring formation. Nat Cell Biol. 2008 Apr;10(4):407-14.
- Franck AD, Powers AF, Gestaut DR, Gonen T, Davis TN, Asbury CL. Tension applied through the Dam1 complex promotes microtubule elongation providing a direct mechanism for length control in mitosis. Nat. Cell. Biol. 2007 Jul;9(7):832-7.
- Shimogawa MM, Graczyk B, Gardner MK, Francis SE, White EA, Ess M, Molk JN, Ruse C, Niessen S, Yates JR 3rd, Muller EG, Bloom K, Odde DJ, Davis TN. Mps1 phosphorylation of Dam1 couples kinetochores to microtubule plus ends at metaphase. Curr Biol. 2006 Aug 8;16(15):1489-501.
- Asbury CL, Gestaut DR, Powers AF, Franck AD, Davis TN. The Dam1 kinetochore complex harnesses microtubule dynamics to produce force and movement. Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9873-8.
- Widlund PO, Lyssand JS, Anderson S, Niessen S, Yates JR 3rd, Davis TN. Phosphorylation of the chromosomal passenger protein Bir1 is required for localization of Ndc10 to the spindle during anaphase and full spindle elongation. Mol Biol Cell. 2006 Mar;17(3):1065-74.
Spindle Pole Body and Centrosome
- Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA. CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Elife. 2021 May 5;10:e65168.
- Fong KK, Davis TN, Asbury CL. Microtubule pivoting enables mitotic spindle assembly in S. cerevisiae. J Cell Biol. 2021 Mar 1;220(3):e202007193.
- King BR, Meehl JB, Vojnar T, Winey M, Muller EG, Davis TN. Microtubule associated proteins and motors required for ectopic microtubule array formation in S. cerevisiae. Genetics. 2021 Jun 24;218(2)
- King BR, Moritz M, Kim H, Agard DA, Asbury CL, Davis TN. XMAP215 and γ-tubulin additively promote microtubule nucleation in purified solutions. Mol. Biol. Cell. 2020 Sep 14.
- Fong KK, Zelter A, Graczyk B, Hoyt JM, Riffle M, Johnson R, MacCoss MJ, Davis TN. Novel phosphorylation states of the yeast spindle pole body. Biol Open. 2018 Jun 14.
- Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG. The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Mol Biol Cell. 2017 Nov 7;28(23):3298-3314.
- Fong KK, Sarangapani KK, Yusko EC, Riffle M, Llauró A, Graczyk B, Davis TN, Asbury CL. Direct measurement of the strength of microtubule attachment to yeast centrosomes. Mol Biol Cell. 2017 Jul 7;28(14):1853-1861.
- Lyon AS, Morin G, Moritz M, Yabut KC, Vojnar T, Zelter A, Muller E, Davis TN, Agard DA. Higher-order oligomerization of Spc110p drives γ-tubulin ring complex assembly. Mol Biol Cell. 2016 Jul 15;27(14):2245-58.
- Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, Agard DA. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nature Structural and Molecular Biology 2015 Feb;22(2):132-7.
- Stoll KE, Brzovic PS, Davis TN, Klevit RE. The essential Ubc4/Ubc5 function in yeast is HECT E3-dependent, and RING E3-dependent pathways require only monoubiquitin transfer by Ubc4. J Biol Chem. 2011 Apr 29;286(17):15165-70.
- Greenland KB, Ding H, Costanzo M, Boone C, Davis TN. Identification of Saccharomyces cerevisiae spindle pole body remodeling factors. PLoS One. 2010 Nov 12;5(11):e15426.
- Kollman JM, Polka JK, Zelter A, Davis TN, Agard DA. Microtubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry. Nature 2010 Aug 12;466(7308):879-82
- Choy RM, Kollman JM, Zelter A, Davis TN, Agard DA. Localization and orientation of the gamma-tubulin small complex components using protein tags as labels for single particle EM. J Struct Biol. 2009 Dec;168(3):571-4
- Kollman JM, Zelter A, Muller EG, Fox B, Rice LM, Davis TN, Agard DA.The structure of the gamma-tubulin small complex: implications of its architecture and fexibility for microtubule nucleation. Mol Biol Cell. 2008 Jan;19(1):207-215.
- Yoder TJ, McElwain MA, Francis SE, Bagley J, Muller EG, Pak B, O’Toole ET, Winey M, Davis TN. Analysis of a spindle pole body mutant reveals a defect in biorientation and illuminates spindle forces. Mol Biol Cell. 2005 Jan;16(1):141-52.
- Flory MR, Davis TN. The centrosomal proteins pericentrin and kendrin are encoded by alternatively spliced products of one gene. Genomics. 2003 Sep;82(3):401-5.
- Yoder TJ, Pearson CG, Bloom K, Davis TN. The Saccharomyces cerevisiae spindle pole body is a dynamic structure. Mol Biol Cell. 2003 Aug;14(8):3494-505.
- Vinh DB, Kern JW, Hancock WO, Howard J, Davis TN. Reconstitution and characterization of budding yeast gamma-tubulin complex. Mol Biol Cell. 2002 Apr;13(4):1144-57.
- Flory MR, Morphew M, Joseph JD, Means AR, Davis TN. Pcp1p, an Spc110p-related calmodulin target at the centrosome of the fission yeast Schizosaccharomyces pombe. Cell Growth Differ. 2002 Feb;13(2):47-58.
- Friedman DB, Kern JW, Huneycutt BJ, Vinh DB, Crawford DK, Steiner E, Scheiltz D, Yates J 3rd, Resing KA, Ahn NG, Winey M, Davis TN. Yeast Mps1p phosphorylates the spindle pole component Spc110p in the N-terminal domain. J Biol Chem. 2001 May 25;276(21):17958-67.
- Flory MR, Moser MJ, Monnat RJ Jr, Davis TN. Identification of a human centrosomal calmodulin-binding protein that shares homology with pericentrin. Proc Natl Acad Sci U S A. 2000 May 23;97(11):5919-23.
- Nguyen T, Vinh DB, Crawford DK, Davis TN. A genetic analysis of interactions with Spc110p reveals distinct functions of Spc97p and Spc98p, components of the yeast gamma-tubulin complex. Mol Biol Cell. 1998 Aug;9(8):2201-16.
- Sundberg HA, Davis TN. A mutational analysis identifies three functional regions of the spindle pole component Spc110p in Saccharomyces cerevisiae. Mol Biol Cell. 1997 Dec;8(12):2575-90.
- Sundberg HA, Goetsch L, Byers B, Davis TN. Role of calmodulin and Spc110p interaction in the proper assembly of spindle pole body components. J Cell Biol. 1996 Apr;133(1):111-24.
- Friedman DB, Sundberg HA, Huang EY, Davis TN. The 110-kD spindle pole body component of Saccharomyces cerevisiae is a phosphoprotein that is modified in a cell cycle-dependent manner. J Cell Biol. 1996 Mar;132(5):903-14.
- Geiser JR, Sundberg HA, Chang BH, Muller EG, Davis TN. The essential mitotic target of calmodulin is the 110-kilodalton component of the spindle pole body in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Dec;13(12):7913-24.
Protein Cross-linking and Adductomics
- Reiter KH, Zelter A, Janowska MK, Riffle M, Shulman N, MacLean BX, Tamura K, Chambers MC, MacCoss MJ, Davis TN, Guttman M, Brzovic PS, Klevit RE. Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain. Structure. 2022 Sep 1;30(9):1269-1284.e6.
- Riffle M, Hoopmann MR, Jaschob D, Zhong G, Moritz RL, MacCoss MJ, Davis TN, Isoherranen N, Zelter A. Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry. Anal Chem. 2022 Mar 1;94(8):3501-3509.
- Riffle M, Jaschob D, Zelter A, Davis TN. Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates. J Proteome Res. 2019 Feb 1;18(2):759-764.
- DaRosa PA, Harrison JS, Zelter A, Davis TN, Brzovic P, Kuhlman B, Klevit RE. A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation. Mol Cell. 2018 Nov 15;72(4):753-765.e6.
- Luan Q, Zelter A, MacCoss MJ, Davis TN, Nolen BJ. Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex. Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1409-E1418.
- Riffle M, Jaschob D, Zelter A, Davis TN. ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. J Proteome Res. 2016 Aug 5;15(8):2863-70.
- Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol. 2016 Jun;194(3):303-10.
- Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN. The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling. Nat Commun. 2015 Nov 12;6:8673.
- Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. Kojak: Efficient analysis of chemically cross-linked protein complexes. J Proteome Res. 2015 Mar 26.
- Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR 3rd, MacCoss MJ, Moritz RL, Asbury CL, Davis TN. Kinetochore Biorientation in Saccharomyces cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex. Genetics. 2014 Dec;198(4):1483-93.
- Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN. Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking. J Proteome Res. 2010 Jul 2;9(7):3583-9.
FRET and Fluorescence Microscopy
Collaborations in the Yeast Resource Center. Learn more about the YRC.
- Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D. Design of a hyperstable 60-subunit protein dodecahedron. Nature. 2016 Jul 7;535(7610):136-9.
- Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A. Determining Protein Complex Structures Based on a Bayesian Model of in Vivo Förster Resonance Energy Transfer (FRET) Data. Mol Cell Proteomics. 2014 Nov;13(11):2812-23.
- Doherty KM, Pride LD, Lukose J, Snydsman BE, Charles R, Pramanik A, Muller EG, Botstein D, Moore CW. Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action. G3 (Bethesda). 2012 Aug;2(8):943-59.
- Ramsden R, Arms L, Davis TN, Muller EG. An intein with genetically selectable markers provides a new approach to internally label proteins with GFP. BMC Biotechnol. 2011 Jun 27;11:71.
- Mathieson EM, Suda Y, Nickas M, Snydsman B, Davis TN, Muller EG, Neiman AM. Vesicle docking to the spindle pole body is necessary to recruit the exocyst during membrane formation in Saccharomyces cerevisiae. Mol Biol Cell. 2010 Nov;21(21):3693-707
- Choy RM, Kollman JM, Zelter A, Davis TN, Agard DA. Localization and orientation of the gamma-tubulin small complex components using protein tags as labels for single particle EM. J Struct Biol. 2009 Dec;168(3):571-4
- Kollman JM, Zelter A, Muller EG, Fox B, Rice LM, Davis TN, Agard DA.The structure of the gamma-tubulin small complex: implications of its architecture and fexibility for microtubule nucleation. Mol Biol Cell. 2008 Jan;19(1):207-215.
- McIntyre J., Muller EGD, Weltzer S, Snydsman BE, Davis TN, Uhlmann F. In vivo analysis of cohesin architecture using FRET in the budding yeast Saccharomyces cerevisiae. EMBO J. 2007 Aug 22;26(16):3783-93.
- Rosenberg JA, Tomlin GC, McDonald WH, Snydsman BE, Muller EG, Yates JR, Gould KL. Ppc89 links multiple proteins, including the septation initiation network, to the core of the fission yeast spindle-pole body. Mol Biol Cell. 2006 Sep;17(9):3793-805.
- Muller EG, Snydsman BE, Novik I, Hailey DW, Gestaut DR, Niemann CA, O’Toole ET, Giddings TH Jr, Sundin BA, Davis TN. The organization of the core proteins of the yeast spindle pole body. Mol Biol Cell. 2005 Jul;16(7):3341-52.
- Flory MR, Carson AR, Muller EG, Aebersold R. An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome. Mol Cell. 2004 Nov 19;16(4):619-30.
- Sundin BA, Chiu CH, Riffle M, Davis TN, Muller EG. Localization of proteins that are coordinately expressed with Cln2 during the cell cycle. Yeast. 2004 Jul 15;21(9):793-800.
- Pot I, Measday V, Snydsman B, Cagney G, Fields S, Davis TN, Muller EG, Hieter P. Chl4p and Iml3p are two new members of the budding yeast outer kinetochore. Mol Biol Cell. 2003 Feb;14(2):460-76.
- Measday V, Hailey DW, Pot I, Givan SA, Hyland KM, Cagney G, Fields S, Davis TN, Hieter P. Ctf3p, the Mis6 budding yeast homolog, interacts with Mcm22p and Mcm16p at the yeast outer kinetochore. Genes Dev. 2002 Jan 1;16(1):101-13.
Yeast Resource Center
Papers from mutli-disciplinary collaborations within the center. Learn more about the YRC.
- Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, Stoddard BL, Fairlie WD, Hockenbery DM, Baker D. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife. 2016 Nov 2;5.
- Han X, Wang Y, Aslanian A, Fonslow B, Graczyk B, Davis TN, Yates JR 3rd. In-line separation by capillary electrophoresis prior to analysis by top-down mass spectrometry enables sensitive characterization of protein complexes. J Proteome Res. 2014 Dec 5;13(12):6078-86.
- Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, Dunham MJ, Maccoss MJ, Akey JM. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Res. 2013 Sep;23(9):1496-504.
- Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R. The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res. 2011 Nov;21(11):1981-94.
- Fonslow BR, Kang SA, Gestaut DR, Graczyk B, Davis TN, Sabatini DM, Yates JR 3rd. Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes. Anal Chem. 2010 Aug 1;82(15):6643-51.
- Malmstrom L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology. PLoS Biol. 2007 Mar 20;5(4):e76
- Hazbun TR, Malmstrom L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, Yates JR 3rd, Davis TN. Assigning function to yeast proteins by integration of technologies. Mol Cell. 2003 Dec;12(6):1353-65.
- Drees BL, Sundin B, Brazeau E, Caviston JP, Chen GC, Guo W, Kozminski KG, Lau MW, Moskow JJ, Tong A, Schenkman LR, McKenzie A 3rd, Brennwald P, Longtine M, Bi E, Chan C, Novick P, Boone C, Pringle JR, Davis TN, Fields S, Drubin DG. A protein interaction map for cell polarity development. J Cell Biol. 2001 Aug 6;154(3):549-71.
Data and Informatics
- Riffle M, Jaschob D, Zelter A, Davis TN. Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates. J Proteome Res. 2019 Feb 1;18(2):759-764.
- Riffle M, Jaschob D, Zelter A, Davis TN. ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. J Proteome Res. 2016 Aug 5;15(8):2863-70.
- Yimit A, Riffle M, Brown GW. Genetic Regulation of Dna2 Localization During the DNA Damage Response. G3 (Bethesda). 2015 Jul 10. pii: g3.115.019208. doi: 10.1534/g3.115.019208. [Epub ahead of print]
- Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ. Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development. J Am Soc Mass Spectrom. 2015 Jul 2. [Epub ahead of print]
- Jaschob D, Davis TN, Riffle M. Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. BMC Res Notes. 2015 Dec;8(1):1009. doi: 10.1186/s13104-015-1009-z. Epub 2015 Mar 7.
- Becker E, Liu Y, Lardenois A, Walther T, Horecka J, Stuparevic I, Law M, Lavigne R, Evrard B, Demougin P, Riffle M, Strich R, Davis RW, Pineau C, Primig M. Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. J Proteomics. 2015 Feb 4. pii: S1874-3919(15)00024-X.
- Jaschob D, Davis TN, Riffle M. SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences. BMC Res Notes. 2014 Jul 23;7:468.
- Sharma V, Eng JK, Maccoss MJ, Riffle M. A mass spectrometry proteomics data management platform. Mol Cell Proteomics. 2012 Sep;11(9):824-31.
- Tkach JM, Yimit A, Lee AY, Riffle M, Costanzo M, Jaschob D, Hendry JA, Ou J, Moffat J, Boone C, Davis TN, Nislow C, Brown GW. Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol. 2012 Sep;14(9):966-76.
- Jaschob D, Riffle M. JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility. Source Code Biol Med. 2012 Jul 30;7(1):8.
- Riffle M, Davis TN. The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. BMC Bioinformatics. 2010 May 19;11:263.
- Hue M, Riffle M, Vert JP, Noble WS. Large-scale prediction of protein-protein interactions from structures. BMC Bioinformatics. 2010 Mar 18;11:144.
- Reynolds SM, Käll L, Riffle ME, Bilmes JA, Noble WS. Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol. 2008 Nov;4(11):e1000213.
- Riffle M, Malmstrom L, Davis TN. The Yeast Resource Center Public Data Repository. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D378-82.
Reviews and Methods
- Hamilton GE, Davis TN. Biochemical evidence for diverse strategies in the inner kinetochore. Open Biol. 2020 Nov;10(11):200284.
- Hamilton G, Dimitrova Y, Davis TN. Seeing is believing: our evolving view of kinetochore structure, composition, and assembly. Curr Opin Cell Biol 2019, 60:44-52.
- Fong KK, Graczyk B, Davis TN. Purification of Fluorescently Labeled Saccharomyces cerevisiae Spindle Pole Bodies. Methods Mol Biol. 2016;1413:189-195.
- Kudalkar EM, Davis TN, Asbury CL. Single-Molecule Total Internal Reflection Fluorescence Microscopy. Cold Spring Harb Protoc. 2016 May 2;2016(5).
- Kudalkar EM, Davis TN, Asbury CL. Preparation of Reactions for Imaging with Total Internal Reflection Fluorescence Microscopy. Cold Spring Harb Protoc. 2016 May 2;2016(5).
- Kudalkar EM, Deng Y, Davis TN, Asbury CL. Coverslip Cleaning and Functionalization for Total Internal Reflection Fluorescence Microscopy. Cold Spring Harb Protoc. 2016 May 2;2016(5).
- Umbreit NT, Davis TN. Mitosis puts sisters in a strained relationship: force generation at the kinetochore. Exp Cell Res. 2012 Jul 15;318(12):1361-6.
- Asbury CL, Tien JF, Davis TN. Kinetochores’ gripping feat: conformational wave or biased diffusion? Trends Cell Biol. 2011 Jan;21(1):38-46.
- Franck AD, Powers AF, Gestaut DR, Davis TN, Asbury CL. Direct physical study of kinetochore-microtubule interactions by reconstitution and interrogation with an optical force clamp. Methods. 2010 Jun;51(2):242-50.
- Gestaut DR, Cooper J, Asbury CL, Davis TN, Wordeman L. Reconstitution and functional analysis of kinetochore subcomplexes. Methods Cell Biol. 2010 May;95:641-56.
- Riffle M, Eng JK. Proteomics data repositories. Proteomics. 2009 Oct;9(20):4653-63.
- Asbury CL, Davis TN. Insights into the kinetochore. Structure. 2008 Jun;16(6):834-6.
- Davis TN, Wordeman L. Rings, bracelets, sleeves, and chevrons: new structures of kinetochore proteins. Trends Cell Biol. 2007 Aug;17(8):377-82
- Davis TN, Muller EGD. Measuring the proximity of proteins in living cells by fluorescence resonance energy transfer between CFP and YFP. Meth. Microbiol. 2007;36:269-280
- Muller EGD, Davis TN. Protein localization by cell imaging. pp. 137-155. In T. D. Veenstra and J. R. Yates, III, (eds) Proteomics for Biological Discovery. 2006. Wiley-Liss, Inc., Hoboken, New Jersey.
- Widlund PO, Davis TN. A high-efficiency method to replace essential genes with mutant alleles in yeast. Yeast. 2005 Jul 30;22(10):769-74.
- Davis TN. Protein localization in proteomics. Curr Opin Chem Biol. 2004 Feb;8(1):49-53.
- Hailey DW, Davis TN, Muller EG. Fluorescence resonance energy transfer using color variants of green fluorescent protein. Methods Enzymol. 2002;351:34-49.
- Nguyen T, Davis TN. Genetic analysis of yeast spindle pole bodies. Methods Cell Biol. 2001;67:95-111.
- Francis SE, Davis TN. The spindle pole body of Saccharomyces cerevisiae: architecture and assembly of the core components. Curr Top Dev Biol. 2000;49:105-32.
- Flory MR, Davis TN. Localization of calmodulin in budding yeast and fission yeast using GFP. Meth. Enzymol. 1999;302:87-102.
- Davis TN. The centrosome on centre stage. Trends in Cell Biol. 1997;7:508-510.
- Davis TN. Calcium in Saccharomyces cerevisiae. Adv Second Messenger Phosphoprotein Res. 1995;30:339-58.
- Davis TN. Mutational analysis of calmodulin in Saccharomyces cerevisiae. Cell Calcium. 1992 Jun-Jul;13(6-7):435-44.
Fork Head Proteins
- Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature. 2000 Jul 6;406(6791):90-4.
- Zhu G, Davis TN. The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes the calmodulin-binding protein in the yeast spindle pole body. Biochim Biophys Acta. 1998 Dec 10;1448(2):236-44.
- Zhu G, Muller EG, Amacher SL, Northrop JL, Davis TN. A dosage-dependent suppressor of a temperature-sensitive calmodulin mutant encodes a protein related to the fork head family of DNA-binding proteins. Mol Cell Biol. 1993 Mar;13(3):1779-87.
Myosin
- Stevens RC, Davis TN. Mlc1p is a light chain for the unconventional myosin Myo2p in Saccharomyces cerevisiae. J Cell Biol. 1998 Aug 10;142(3):711-22.
- Brockerhoff SE, Stevens RC, Davis TN. The unconventional myosin, Myo2p, is a calmodulin target at sites of cell growth in Saccharomyces cerevisiae. J Cell Biol. 1994 Feb;124(3):315-23.
- Brockerhoff SE, Davis TN. Calmodulin concentrates at regions of cell growth in Saccharomyces cerevisiae. J Cell Biol. 1992 Aug;118(3):619-29.
Calmodulin
- Moser MJ, Flory MR, Davis TN. Calmodulin localizes to the spindle pole body of Schizosaccharomyces pombe and performs an essential function in chromosome segregation. J Cell Sci. 1997 Aug;110 ( Pt 15):1805-12.
- Moser MJ, Geiser JR, Davis TN. Ca2+-calmodulin promotes survival of pheromone-induced growth arrest by activation of calcineurin and Ca2+-calmodulin-dependent protein kinase. Mol Cell Biol. 1996 Sep;16(9):4824-31.
- Moser MJ, Lee SY, Klevit RE, Davis TN. Ca2+ binding to calmodulin and its role in Schizosaccharomyces pombe as revealed by mutagenesis and NMR spectroscopy. J Biol Chem. 1995 Sep 1;270(35):20643-52.
- Starovasnik MA, Davis TN, Klevit RE. Similarities and differences between yeast and vertebrate calmodulin: an examination of the calcium-binding and structural properties of calmodulin from the yeast Saccharomyces cerevisiae. Biochemistry. 1993 Apr 6;32(13):3261-70.
- Davis TN. A temperature-sensitive calmodulin mutant loses viability during mitosis. J Cell Biol. 1992 Aug;118(3):607-17.
- Brockerhoff SE, Edmonds CG, Davis TN. Structural analysis of wild-type and mutant yeast calmodulins by limited proteolysis and electrospray ionization mass spectrometry. Protein Sci. 1992 Apr;1(4):504-16.
- Geiser JR, van Tuinen D, Brockerhoff SE, Neff MM, Davis TN. Can calmodulin function without binding calcium? Cell. 1991 Jun 14;65(6):949-59.
- Persechini A, Kretsinger RH, Davis TN. Calmodulins with deletions in the central helix functionally replace the native protein in yeast cells. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):449-52.
- Davis TN, Thorner J. Vertebrate and yeast calmodulin, despite significant sequence divergence, are functionally interchangeable. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7909-13.
- Davis TN, Urdea MS, Masiarz FR, Thorner J. Isolation of the yeast calmodulin gene: Calmodulin is an essential protein.Cell. 1986 Nov 7;47(3):423-31.