piwik-script

Center for Computational and Theoretical Biology

Jörg Schultz

Prof. Dr. Jörg Schultz

Group Leader at the CCTB

and

Professor for Bioinformatics

Department of Bioinformatics, Biocenter, University Würzburg

Tel: 0931 - 31 84553

eMail: Joerg.Schultz@uni-wuerzburg.de

Research

There are just two questions to be asked in evolution:

How are things related - and what makes them differ?

  AM Dean EMBO reports (2010) 11, 409

Curriculum Vitae

2015 - 2019 Managing Board Center for Computational and Theoretical Biology, University Würzburg
2004 - now Co-opted Faculty for Mathematics and Informatics, University Würzburg
2003 - now C3 Professor for Bioinformatics Faculty of Biology, University Würzburg
2002 - 2003 Groupleader Max-Planck-Institut for Molecular Genetics, Department Computational Molecular Biology, Berlin
2000 - 2002 Groupleader Bioinformatics cellzome, Heidelberg
1996 - 2000 PhD student (PreDoc) EMBL Heidelberg
1995 - 1996 Diploma thesis EMBL Heidelberg
1991 - 1996 Study of biology at the university of Konstanz  

Publications

2020[ to top ]
  • Iosip, A. L., Böhm, J., Scherzer, S., Al-Rasheid, K. A. S., Dreyer, I., Schultz, J., Becker, D., Kreuzer, I., & Hedrich, R. {{T}he {V}enus flytrap trigger hair-specific potassium channel {K}{D}{M}1 can reestablish the {K}+ gradient required for hapto-electric signaling}. PLoS Biol, 18(12), e3000964.
  • Dreyer, I., Sussmilch, F. C., Fukushima, K., Riadi, G., Becker, D., Schultz, J., & Hedrich, R. {{H}ow to {G}row a {T}ree: {P}lant {V}oltage-{D}ependent {C}ation {C}hannels in the {S}potlight of {E}volution}. Trends Plant Sci.
  • Palfalvi, G., Hackl, T., Terhoeven, N., Shibata, T. F., Nishiyama, T., Ankenbrand, M., Becker, D., Förster, F., Freund, M., Iosip, A., Kreuzer, I., Saul, F., Kamida, C., Fukushima, K., Shigenobu, S., Tamada, Y., Adamec, L., Hoshi, Y., Ueda, K., Winkelmann, T., Fuchs, J., Schubert, I., Schwacke, R., Al-Rasheid, K., Schultz, J., Hasebe, M., & Hedrich, R. {{G}enomes of the {V}enus {F}lytrap and {C}lose {R}elatives {U}nveil the {R}oots of {P}lant {C}arnivory}. Curr Biol, 30(12), 2312-2320.
  • Keller, A., Hohlfeld, S., Kolter, A., Schultz, J., Gemeinholzer, B., & Ankenbrand, M. J. BCdatabaser: on-the-fly reference database creation for DNA (meta-)barcoding. Bioinformatics, in press.
2019[ to top ]
  • Sickel, W., Van de Weyer, A. L., Bemm, F., Schultz, J., & Keller, A. {{V}enus flytrap microbiotas withstand harsh conditions during prey digestion}. FEMS Microbiol. Ecol., 95(3), Article 3.
  • Sussmilch, F. C., Schultz, J., Hedrich, R., & Roelfsema, M. R. G. {{A}cquiring {C}ontrol: {T}he {E}volution of {S}tomatal {S}ignalling {P}athways}. Trends Plant Sci., 24(4), 342-351.
2018[ to top ]
  • Terhoeven, N., Schultz, J., & Hackl, T. reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. Journal of Open Source Software, 3(22), 527. https://doi.org/https://doi.org/10.21105/joss.00527
2016[ to top ]
  • Brinkmann, K., Winterhoff, M., Onel, S. F., Schultz, J., Faix, J., & Bogdan, S. {{W}{H}{A}{M}{Y} is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in {D}rosophila}. J. Cell. Sci., 129(3), 604-620.
  • Bemm, F., Becker, D., Larisch, C., Kreuzer, I., Escalante-Perez, M., Schulze, W. X., Ankenbrand, M., Van de Weyer, A. L., Krol, E., Al-Rasheid, K. A., Mithofer, A., Weber, A. P., Schultz, J., & Hedrich, R. {{V}enus flytrap carnivorous lifestyle builds on herbivore defense strategies}. Genome Res., 26(6), 812-825.
  • Bemm, F., Weiss, C. L., Schultz, J., & Forster, F. {{G}enome of a tardigrade: {H}orizontal gene transfer or bacterial contamination?}. Proc. Natl. Acad. Sci. U.S.A.
  • Ja?lan, D., Mueller, T. D., Becker, D., Schultz, J., Cuin, T. A., Marten, I., Dreyer, I., Schonknecht, G., & Hedrich, R. {{G}ating of the two-pore cation channel {A}t{T}{P}{C}1 in the plant vacuole is based on a single voltage-sensing domain}. Plant Biol (Stuttg), 18(5), 750-760.
  • Schwarz, R. F., Tamuri, A. U., Kultys, M., King, J., Godwin, J., Florescu, A. M., Schultz, J., & Goldman, N. {{A}{L}{V}{I}{S}: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments}. Nucleic Acids Res., 44(8), e77.
2015[ to top ]
  • Ankenbrand, M. J., Keller, A., Wolf, M., Schultz, J., & Forster, F. {{I}{T}{S}2 {D}atabase {V}: {T}wice as {M}uch}. Mol. Biol. Evol., 32(11), 3030-3032.
  • Weiss, C., & Schultz, J. {{I}dentification of divergent {W}{H}2 motifs by {H}{M}{M}-{H}{M}{M} alignments}. BMC Res Notes, 8(1), 18.
2014[ to top ]
  • Keller, D. B., & Schultz, J. {{W}ord formation is aware of morpheme family size}. PLoS ONE, 9(4), e93978.
  • Baier, H., & Schultz, J. {{I}{S}{A}{A}{C} - {I}nter{S}pecies {A}nalysing {A}pplication using {C}ontainers}. BMC Bioinformatics, 15(1), 18.
  • Bechtold, M., Schultz, J., & Bogdan, S. {{F}{H}{O}{D} proteins in actin dynamics-a formin’ class of its own}. Small GTPases, 5(2), 1-6.
  • Seifried, A., Knobloch, G., Duraphe, P. S., Segerer, G., Manhard, J., Schindelin, H., Schultz, J., & Gohla, A. {{E}volutionary and {S}tructural {A}nalyses of the {M}ammalian {H}aloacid {D}ehalogenase-{T}ype {P}hosphatases {A}{U}{M} and {C}hronophin {P}rovide {I}nsight into the {B}asis of their {D}ifferent {S}ubstrate {S}pecificities}. J. Biol. Chem., 289(6), 3416-31.
  • Keller, A., Horn, H., Forster, F., & Schultz, J. {{C}omputational integration of genomic traits into 16{S} r{D}{N}{A} microbiota sequencing studies}. Gene.
  • Hackl, T., Hedrich, R., Schultz, J., & Forster, F. {proovread: large-scale high-accuracy {P}ac{B}io correction through iterative short read consensus}. Bioinformatics.
2013[ to top ]
  • Schultz, J., & Terhoeven, N. {{T}he bilaterian roots of cordon-bleu}. BMC Res Notes, 6(1), 393.
  • Seifried, A., Schultz, J., & Gohla, A. {{H}uman {H}{A}{D} phosphatases: structure, mechanism, and roles in health and disease}. FEBS J., 280(2), 549-571.
  • Keller, D. B., & Schultz, J. {{C}onnectivity, not frequency, determines the fate of a morpheme}. PLoS ONE, 8(7), e69945.
  • Bogdan, S., Schultz, J., & Grosshans, J. Formin’ cellular structures. Communicative & Integrative Biology, 6(6), e27634.
2012[ to top ]
  • Merget, B., Koetschan, C., Hackl, T., Forster, F., Dandekar, T., Muller, T., Schultz, J., & Wolf, M. {{T}he {I}{T}{S}2 {D}atabase}. J Vis Exp, 61, Article 61.
  • Schulze, W. X., Sanggaard, K. W., Kreuzer, I., Knudsen, A. D., Bemm, F., Th?gersen, I. B., Brautigam, A., Thomsen, L. R., Schliesky, S., Dyrlund, T. F., Escalante-Perez, M., Becker, D., Schultz, J., Karring, H., Weber, A., H?jrup, P., Hedrich, R., & Enghild, J. J. {{T}he protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms}. Mol. Cell Proteomics, 11(11), 1306-1319.
  • Koetschan, C., Hackl, T., Muller, T., Wolf, M., Forster, F., & Schultz, J. {{I}{T}{S}2 database {I}{V}: interactive taxon sampling for internal transcribed spacer 2 based phylogenies}. Mol. Phylogenet. Evol., 63(3), 585-588.
  • Keller, D. B., & Schultz, J. Morpheme networks reveal language dynamics. Actes Des 11es Journées Internationales d’Analyse Statistique Des Données Textuelles Proceedings of the 11th International Conference on the Statistical Analysis of Textual Data.
2010[ to top ]
  • Koetschan, C., Forster, F., Keller, A., Schleicher, T., Ruderisch, B., Schwarz, R., Muller, T., Wolf, M., & Schultz, J. {{T}he {I}{T}{S}2 {D}atabase {I}{I}{I}--sequences and structures for phylogeny}. Nucleic Acids Res., 38, D275-279.
  • Pinkert, S., Schultz, J., & Reichardt, J. {{P}rotein interaction networks--more than mere modules}. PLoS Comput. Biol., 6, e1000659.
  • Keller, A., Forster, F., Muller, T., Dandekar, T., Schultz, J., & Wolf, M. {{I}ncluding {R}{N}{A} secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees}. Biol. Direct, 5, 4.
  • Schwarz, R. F., Fletcher, W., Forster, F., Merget, B., Wolf, M., Schultz, J., & Markowetz, F. {{E}volutionary distances in the twilight zone--a rational kernel approach}. PLoS ONE, 5, e15788.
2009[ to top ]
  • Kroiss, M., Fischer, U., & Schultz, J. {{W}hen one plus one equals three: biochemistry and bioinformatics combine to answer complex questions}. Fly (Austin), 3, 210-212.
  • Schwalie, P. C., & Schultz, J. {{P}ositive selection in tick saliva proteins of the {S}alp15 family}. J. Mol. Evol., 68, 186-191.
  • Georgi, B., Schultz, J., & Schliep, A. {{P}artially-supervised protein subclass discovery with simultaneous annotation of functional residues}. BMC Struct. Biol., 9, 68.
  • Schultz, J., & Wolf, M. {{I}{T}{S}2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics}. Mol. Phylogenet. Evol., 52, 520-523.
  • Seidl, M. F., & Schultz, J. {{E}volutionary flexibility of protein complexes}. BMC Evol. Biol., 9, 155.
  • Schwarz, R., Seibel, P. N., Rahmann, S., Schoen, C., Huenerberg, M., Muller-Reible, C., Dandekar, T., Karchin, R., Schultz, J., & Muller, T. {{D}etecting species-site dependencies in large multiple sequence alignments}. Nucleic Acids Res., 37, 5959-5968.
  • Bemm, F., Schwarz, R., Forster, F., & Schultz, J. {{A} kinome of 2600 in the ciliate {P}aramecium tetraurelia}. FEBS Lett., 583, 3589-3592.
  • Keller, A., Schleicher, T., Schultz, J., Muller, T., Dandekar, T., & Wolf, M. {5.8{S}-28{S} r{R}{N}{A} interaction and {H}{M}{M}-based {I}{T}{S}2 annotation}. Gene, 430, 50-57.
2008[ to top ]
  • Selig, C., Wolf, M., Muller, T., Dandekar, T., & Schultz, J. {{T}he {I}{T}{S}2 {D}atabase {I}{I}: homology modelling {R}{N}{A} structure for molecular systematics}. Nucleic Acids Res., 36, D377-380.
  • Wolf, M., Ruderisch, B., Dandekar, T., Schultz, J., & Muller, T. {{P}rof{D}ist{S}: (profile-) distance based phylogeny on sequence--structure alignments}. Bioinformatics, 24, 2401-2402.
  • Perotti, C., Liu, R., Parusel, C. T., Bocher, N., Schultz, J., Bork, P., Pfitzner, E., Groner, B., & Shemanko, C. S. {{H}eat shock protein-90-alpha, a prolactin-{S}{T}{A}{T}5 target gene identified in breast cancer cells, is involved in apoptosis regulation}. Breast Cancer Res., 10, R94.
  • Blenk, S., Engelmann, J. C., Pinkert, S., Weniger, M., Schultz, J., Rosenwald, A., Muller-Hermelink, H. K., Muller, T., & Dandekar, T. {{E}xplorative data analysis of {M}{C}{L} reveals gene expression networks implicated in survival and prognosis supported by explorative {C}{G}{H} analysis}. BMC Cancer, 8, 106.
  • Kroiss, M., Schultz, J., Wiesner, J., Chari, A., Sickmann, A., & Fischer, U. {{E}volution of an {R}{N}{P} assembly system: a minimal {S}{M}{N} complex facilitates formation of {U}sn{R}{N}{P}s in {D}rosophila melanogaster}. Proc. Natl. Acad. Sci. U.S.A., 105, 10045-10050.
2007[ to top ]
  • Blenk, S., Engelmann, J., Weniger, M., Schultz, J., Dittrich, M., Rosenwald, A., Muller-Hermelink, H. K., Muller, T., & Dandekar, T. {{G}erminal center {B} cell-like ({G}{C}{B}) and activated {B} cell-like ({A}{B}{C}) type of diffuse large {B} cell lymphoma ({D}{L}{B}{C}{L}): analysis of molecular predictors, signatures, cell cycle state and patient survival}. Cancer Inform, 3, 399-420.
  • Weniger, M., Engelmann, J. C., & Schultz, J. {{G}enome {E}xpression {P}athway {A}nalysis {T}ool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context}. BMC Bioinformatics, 8, 179.
  • Zemojtel, T., Penzkofer, T., Schultz, J., Dandekar, T., Badge, R., & Vingron, M. {{E}xonization of active mouse {L}1s: a driver of transcriptome evolution?}. BMC Genomics, 8, 392.
  • Muller, T., Philippi, N., Dandekar, T., Schultz, J., & Wolf, M. {{D}istinguishing species}. RNA, 13, 1469-1472.
2006[ to top ]
  • Schultz, J., Muller, T., Achtziger, M., Seibel, P. N., Dandekar, T., & Wolf, M. {{T}he internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses}. Nucleic Acids Res., 34, W704-707.
  • Letunic, I., Copley, R. R., Pils, B., Pinkert, S., Schultz, J., & Bork, P. {{S}{M}{A}{R}{T} 5: domains in the context of genomes and networks}. Nucleic Acids Res., 34, D257-260.
  • Friedrich, T., Pils, B., Dandekar, T., Schultz, J., & Muller, T. {{M}odelling interaction sites in protein domains with interaction profile hidden {M}arkov models}. Bioinformatics, 22, 2851-2857.
  • Gandhi, T. K., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S., & Pandey, A. {{A}nalysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets}. Nat. Genet., 38, 285-293.
  • Seibel, P. N., Muller, T., Dandekar, T., Schultz, J., & Wolf, M. {4{S}{A}{L}{E}--a tool for synchronous {R}{N}{A} sequence and secondary structure alignment and editing}. BMC Bioinformatics, 7, 498.
2005[ to top ]
  • Pils, B., Copley, R. R., & Schultz, J. {{V}ariation in structural location and amino acid conservation of functional sites in protein domain families}. BMC Bioinformatics, 6, 210.
  • Bussow, K., Scheich, C., Sievert, V., Harttig, U., Schultz, J., Simon, B., Bork, P., Lehrach, H., & Heinemann, U. {{S}tructural genomics of human proteins--target selection and generation of a public catalogue of expression clones}. Microb. Cell Fact., 4, 21.
  • Wolf, M., Achtziger, M., Schultz, J., Dandekar, T., & Muller, T. {{H}omology modeling revealed more than 20,000 r{R}{N}{A} internal transcribed spacer 2 ({I}{T}{S}2) secondary structures}. RNA, 11, 1616-1623.
  • Schultz, J., Maisel, S., Gerlach, D., Muller, T., & Wolf, M. {{A} common core of secondary structure of the internal transcribed spacer 2 ({I}{T}{S}2) throughout the {E}ukaryota}. RNA, 11, 361-364.
2004[ to top ]
  • Letunic, I., Copley, R. R., Schmidt, S., Ciccarelli, F. D., Doerks, T., Schultz, J., Ponting, C. P., & Bork, P. {{S}{M}{A}{R}{T} 4.0: towards genomic data integration}. Nucleic Acids Res., 32, D142-144.
  • Pils, B., & Schultz, J. {{I}nactive enzyme-homologues find new function in regulatory processes}. J. Mol. Biol., 340, 399-404.
  • Schultz, J. {{H}{T}{T}{M}, a horizontally transferred transmembrane domain}. Trends Biochem. Sci., 29, 4-7.
  • Schuster-Bockler, B., Schultz, J., & Rahmann, S. {{H}{M}{M} {L}ogos for visualization of protein families}. BMC Bioinformatics, 5, 7.
  • Pils, B., & Schultz, J. {{E}volution of the multifunctional protein tyrosine phosphatase family}. Mol. Biol. Evol., 21, 625-631.
  • Zemojtel, T., Penzkofer, T., Dandekar, T., & Schultz, J. {{A} novel conserved family of nitric oxide synthase?}. Trends Biochem. Sci., 29, 224-226.
2002[ to top ]
  • Doerks, T., Copley, R. R., Schultz, J., Ponting, C. P., & Bork, P. {{S}ystematic identification of novel protein domain families associated with nuclear functions}. Genome Res., 12, 47-56.
  • Copley, R. R., Ponting, C. P., Schultz, J., & Bork, P. {{S}equence analysis of multidomain proteins: past perspectives and future directions}. Adv. Protein Chem., 61, 75-98.
  • Letunic, I., Goodstadt, L., Dickens, N. J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R. R., Ponting, C. P., & Bork, P. {{R}ecent improvements to the {S}{M}{A}{R}{T} domain-based sequence annotation resource}. Nucleic Acids Res., 30, 242-244.
  • Schultz, J., & Pils, B. {{P}rediction of structure and functional residues for {O}-{G}lc{N}{A}case, a divergent homologue of acetyltransferases}. FEBS Lett., 529, 179-182.
  • Mott, R., Schultz, J., Bork, P., & Ponting, C. P. {{P}redicting protein cellular localization using a domain projection method}. Genome Res., 12, 1168-1174.
  • Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S. E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M. R., Brown, D. G., Brown, S. D., Bult, C., Burton, J., Butler, J., Campbell, R. D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A. T., Church, D. M., Clamp, M., Clee, C., Collins, F. S., Cook, L. L., Copley, R. R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K. D., Deri, J., Dermitzakis, E. T., Dewey, C., Dickens, N. J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D. M., Eddy, S. R., Elnitski, L., Emes, R. D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G. A., Flicek, P., Foley, K., Frankel, W. N., Fulton, L. A., Fulton, R. S., Furey, T. S., Gage, D., Gibbs, R. A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T. A., Green, E. D., Gregory, S., Guigo, R., Guyer, M., Hardison, R. C., Haussler, D., Hayashizaki, Y., Hillier, L. W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D. B., Johnson, L. S., Jones, M., Jones, T. A., Joy, A., Kamal, M., Karlsson, E. K., Karolchik, D., Kasprzyk, A., Kawai, J., Keibler, E., Kells, C., Kent, W. J., Kirby, A., Kolbe, D. L., Korf, I., Kucherlapati, R. S., Kulbokas, E. J., Kulp, D., Landers, T., Leger, J. P., Leonard, S., Letunic, I., Levine, R., Li, J., Li, M., Lloyd, C., Lucas, S., Ma, B., Maglott, D. R., Mardis, E. R., Matthews, L., Mauceli, E., Mayer, J. H., McCarthy, M., McCombie, W. R., McLaren, S., McLay, K., McPherson, J. D., Meldrim, J., Meredith, B., Mesirov, J. P., Miller, W., Miner, T. L., Mongin, E., Montgomery, K. T., Morgan, M., Mott, R., Mullikin, J. C., Muzny, D. M., Nash, W. E., Nelson, J. O., Nhan, M. N., Nicol, R., Ning, Z., Nusbaum, C., O’Connor, M. J., Okazaki, Y., Oliver, K., Overton-Larty, E., Pachter, L., Parra, G., Pepin, K. H., Peterson, J., Pevzner, P., Plumb, R., Pohl, C. S., Poliakov, A., Ponce, T. C., Ponting, C. P., Potter, S., Quail, M., Reymond, A., Roe, B. A., Roskin, K. M., Rubin, E. M., Rust, A. G., Santos, R., Sapojnikov, V., Schultz, B., Schultz, J., Schwartz, M. S., Schwartz, S., Scott, C., Seaman, S., Searle, S., Sharpe, T., Sheridan, A., Shownkeen, R., Sims, S., Singer, J. B., Slater, G., Smit, A., Smith, D. R., Spencer, B., Stabenau, A., Stange-Thomann, N., Sugnet, C., Suyama, M., Tesler, G., Thompson, J., Torrents, D., Trevaskis, E., Tromp, J., Ucla, C., Ureta-Vidal, A., Vinson, J. P., Niederhausern, A. C. V., Wade, C. M., Wall, M., Weber, R. J., Weiss, R. B., Wendl, M. C., West, A. P., Wetterstrand, K., Wheeler, R., Whelan, S., Wierzbowski, J., Willey, D., Williams, S., Wilson, R. K., Winter, E., Worley, K. C., Wyman, D., Yang, S., Yang, S. P., Zdobnov, E. M., Zody, M. C., & Lander, E. S. {{I}nitial sequencing and comparative analysis of the mouse genome}. Nature, 420, 520-562.
  • Dimopoulos, G., Christophides, G. K., Meister, S., Schultz, J., White, K. P., Barillas-Mury, C., & Kafatos, F. C. {{G}enome expression analysis of {A}nopheles gambiae: responses to injury, bacterial challenge, and malaria infection}. Proc. Natl. Acad. Sci. U.S.A., 99, 8814-8819.
  • Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., & Superti-Furga, G. {{F}unctional organization of the yeast proteome by systematic analysis of protein complexes}. Nature, 415, 141-147.
2001[ to top ]
  • Schultz, J., Jones, T., Bork, P., Sheer, D., Blencke, S., Steyrer, S., Wellbrock, U., Bevec, D., Ullrich, A., & Wallasch, C. {{M}olecular characterization of a c{D}{N}{A} encoding functional human {C}{L}{K}4 kinase and localization to chromosome 5q35 [correction of 4q35]}. Genomics, 71, 368-370.
  • Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J. P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J. C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R. H., Wilson, R. K., Hillier, L. W., McPherson, J. D., Marra, M. A., Mardis, E. R., Fulton, L. A., Chinwalla, A. T., Pepin, K. H., Gish, W. R., Chissoe, S. L., Wendl, M. C., Delehaunty, K. D., Miner, T. L., Delehaunty, A., Kramer, J. B., Cook, L. L., Fulton, R. S., Johnson, D. L., Minx, P. J., Clifton, S. W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J. F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R. A., Muzny, D. M., Scherer, S. E., Bouck, J. B., Sodergren, E. J., Worley, K. C., Rives, C. M., Gorrell, J. H., Metzker, M. L., Naylor, S. L., Kucherlapati, R. S., Nelson, D. L., Weinstock, G. M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Smith, D. R., Doucette-Stamm, L., Rubenfield, M., Weinstock, K., Lee, H. M., Dubois, J., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S., Davis, R. W., Federspiel, N. A., Abola, A. P., Proctor, M. J., Myers, R. M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D. R., Olson, M. V., Kaul, R., Raymond, C., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G. A., Athanasiou, M., Schultz, R., Roe, B. A., Chen, F., Pan, H., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W. R., de la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J. A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D. G., Burge, C. B., Cerutti, L., Chen, H. C., Church, D., Clamp, M., Copley, R. R., Doerks, T., Eddy, S. R., Eichler, E. E., Furey, T. S., Galagan, J., Gilbert, J. G., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L. S., Jones, T. A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W. J., Kitts, P., Koonin, E. V., Korf, I., Kulp, D., Lancet, D., Lowe, T. M., McLysaght, A., Mikkelsen, T., Moran, J. V., Mulder, N., Pollara, V. J., Ponting, C. P., Schuler, G., Schultz, J., Slater, G., Smit, A. F., Stupka, E., Szustakowski, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y. I., Wolfe, K. H., Yang, S. P., Yeh, R. F., Collins, F., Guyer, M. S., Peterson, J., Felsenfeld, A., Wetterstrand, K. A., Patrinos, A., Morgan, M. J., de Jong, P., Catanese, J. J., Osoegawa, K., Shizuya, H., Choi, S., Chen, Y. J., & Szustakowki, J. {{I}nitial sequencing and analysis of the human genome}. Nature, 409, 860-921.
2000[ to top ]
  • Schultz, J., Copley, R. R., Doerks, T., Ponting, C. P., & Bork, P. {{S}{M}{A}{R}{T}: a web-based tool for the study of genetically mobile domains}. Nucleic Acids Res., 28, 231-234.
  • Schultz, J., Doerks, T., Ponting, C. P., Copley, R. R., & Bork, P. {{M}ore than 1,000 putative new human signalling proteins revealed by {E}{S}{T} data mining}. Nat. Genet., 25, 201-204.
  • Ponting, C. P., Schultz, J., Copley, R. R., Andrade, M. A., & Bork, P. {{E}volution of domain families}. Adv. Protein Chem., 54, 185-244.
  • Dimopoulos, G., Casavant, T. L., Chang, S., Scheetz, T., Roberts, C., Donohue, M., Schultz, J., Benes, V., Bork, P., Ansorge, W., Soares, M. B., & Kafatos, F. C. {{A}nopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines}. Proc. Natl. Acad. Sci. U.S.A., 97, 6619-6624.
1999[ to top ]
  • Ponting, C. P., Schultz, J., Milpetz, F., & Bork, P. {{S}{M}{A}{R}{T}: identification and annotation of domains from signalling and extracellular protein sequences}. Nucleic Acids Res., 27, 229-232.
  • Copley, R. R., Schultz, J., Ponting, C. P., & Bork, P. {{P}rotein families in multicellular organisms}. Curr. Opin. Struct. Biol., 9, 408-415.
  • Ponting, C. P., Bork, P., Schultz, J., & Aravind, L. {{N}o {S}ec7-homology domain in guanine-nucleotide-exchange factors that act on {R}as and {R}ho}. Trends Biochem. Sci., 24, 177-178.
  • Ponting, C. P., Aravind, L., Schultz, J., Bork, P., & Koonin, E. V. {{E}ukaryotic signalling domain homologues in archaea and bacteria. {A}ncient ancestry and horizontal gene transfer}. J. Mol. Biol., 289, 729-745.
1998[ to top ]
  • Schultz, J., Milpetz, F., Bork, P., & Ponting, C. P. {{S}{M}{A}{R}{T}, a simple modular architecture research tool: identification of signaling domains}. Proc. Natl. Acad. Sci. U.S.A., 95, 5857-5864.
1997[ to top ]
  • Ponting, C., Schultz, J., & Bork, P. {{S}{P}{R}{Y} domains in ryanodine receptors ({C}a(2+)-release channels)}. Trends Biochem. Sci., 22, 193-194.
  • Schultz, J., Ponting, C. P., Hofmann, K., & Bork, P. {{S}{A}{M} as a protein interaction domain involved in developmental regulation}. Protein Sci., 6, 249-253.
  • Yuan, Y. P., Schultz, J., Mlodzik, M., & Bork, P. {{S}ecreted fringe-like signaling molecules may be glycosyltransferases}. Cell, 88, 9-11.
  • Bork, P., Schultz, J., & Ponting, C. P. {{C}ytoplasmic signalling domains: the next generation}. Trends Biochem. Sci., 22, 296-298.
1996[ to top ]
  • Bork, P., Brown, N. P., Hegyi, H., & Schultz, J. {{T}he protein phosphatase 2{C} ({P}{P}2{C}) superfamily: detection of bacterial homologues}. Protein Sci., 5, 1421-1425.