Chair 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 ]
  • {{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}. Dreyer, I.; Sussmilch, F. C.; Fukushima, K.; Riadi, G.; Becker, D.; Schultz, J.; Hedrich, R. In Trends Plant Sci. 2020.
  • {{T}he {V}enus flytrap trigger hair-specific potassium channel {K}{D}{M}1 can reestablish the {K}+ gradient required for hapto-electric signaling}. Iosip, A. L.; Böhm, J.; Scherzer, S.; Al-Rasheid, K. A. S.; Dreyer, I.; Schultz, J.; Becker, D.; Kreuzer, I.; Hedrich, R. In PLoS Biol, 18(12), bl. e3000964. 2020.
  • BCdatabaser: on-the-fly reference database creation for DNA (meta-)barcoding. Keller, Alexander; Hohlfeld, Sonja; Kolter, Andreas; Schultz, Jörg; Gemeinholzer, Birgit; Ankenbrand, Markus J. In Bioinformatics, bl. in press. 2020.
  • {{G}enomes of the {V}enus {F}lytrap and {C}lose {R}elatives {U}nveil the {R}oots of {P}lant {C}arnivory}. 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. In Curr Biol, 30(12), ble. 2312–2320. 2020.
2019[ to top ]
  • {{A}cquiring {C}ontrol: {T}he {E}volution of {S}tomatal {S}ignalling {P}athways}. Sussmilch, F. C.; Schultz, J.; Hedrich, R.; Roelfsema, M. R. G. In Trends Plant Sci., 24(4), ble. 342–351. 2019.
  • {{V}enus flytrap microbiotas withstand harsh conditions during prey digestion}. Sickel, W.; Van de Weyer, A. L.; Bemm, F.; Schultz, J.; Keller, A. In FEMS Microbiol. Ecol., 95(3). 2019.
2018[ to top ]
  • reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. Terhoeven, Niklas; Schultz, Jörg; Hackl, Thomas. In Journal of Open Source Software, 3(22), bl. 527. 2018.
2016[ to top ]
  • {{V}enus flytrap carnivorous lifestyle builds on herbivore defense strategies}. 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. In Genome Res., 26(6), ble. 812–825. 2016.
  • {{G}enome of a tardigrade: {H}orizontal gene transfer or bacterial contamination?}. Bemm, F.; Weiss, C. L.; Schultz, J.; Forster, F. In Proc. Natl. Acad. Sci. U.S.A. 2016.
  • {{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}. Ja?lan, D.; Mueller, T. D.; Becker, D.; Schultz, J.; Cuin, T. A.; Marten, I.; Dreyer, I.; Schonknecht, G.; Hedrich, R. In Plant Biol (Stuttg), 18(5), ble. 750–760. 2016.
  • {{A}{L}{V}{I}{S}: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments}. Schwarz, R. F.; Tamuri, A. U.; Kultys, M.; King, J.; Godwin, J.; Florescu, A. M.; Schultz, J.; Goldman, N. In Nucleic Acids Res., 44(8), bl. e77. 2016.
  • {{W}{H}{A}{M}{Y} is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in {D}rosophila}. Brinkmann, K.; Winterhoff, M.; Onel, S. F.; Schultz, J.; Faix, J.; Bogdan, S. In J. Cell. Sci., 129(3), ble. 604–620. 2016.
2015[ to top ]
  • {{I}dentification of divergent {W}{H}2 motifs by {H}{M}{M}-{H}{M}{M} alignments}. Weiss, C.; Schultz, J. In BMC Res Notes, 8(1), bl. 18. 2015.
  • {{I}{T}{S}2 {D}atabase {V}: {T}wice as {M}uch}. Ankenbrand, M. J.; Keller, A.; Wolf, M.; Schultz, J.; Forster, F. In Mol. Biol. Evol., 32(11), ble. 3030–3032. 2015.
2014[ to top ]
  • {{I}{S}{A}{A}{C} - {I}nter{S}pecies {A}nalysing {A}pplication using {C}ontainers}. Baier, H.; Schultz, J. In BMC Bioinformatics, 15(1), bl. 18. 2014.
  • {{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}. Seifried, A.; Knobloch, G.; Duraphe, P. S.; Segerer, G.; Manhard, J.; Schindelin, H.; Schultz, J.; Gohla, A. In J. Biol. Chem., 289(6), ble. 3416–31. 2014.
  • {{F}{H}{O}{D} proteins in actin dynamics-a formin’ class of its own}. Bechtold, M.; Schultz, J.; Bogdan, S. In Small GTPases, 5(2), ble. 1–6. 2014.
  • {proovread: large-scale high-accuracy {P}ac{B}io correction through iterative short read consensus}. Hackl, T.; Hedrich, R.; Schultz, J.; Forster, F. In Bioinformatics. 2014.
  • {{W}ord formation is aware of morpheme family size}. Keller, D. B.; Schultz, J. In PLoS ONE, 9(4), bl. e93978. 2014.
  • {{C}omputational integration of genomic traits into 16{S} r{D}{N}{A} microbiota sequencing studies}. Keller, A.; Horn, H.; Forster, F.; Schultz, J. In Gene. 2014.
2013[ to top ]
  • {{H}uman {H}{A}{D} phosphatases: structure, mechanism, and roles in health and disease}. Seifried, A.; Schultz, J.; Gohla, A. In FEBS J., 280(2), ble. 549–571. 2013.
  • Formin’ cellular structures. Bogdan, Sven; Schultz, Jörg; Grosshans, Jörg. In Communicative & Integrative Biology, 6(6), bl. e27634. 2013.
  • {{C}onnectivity, not frequency, determines the fate of a morpheme}. Keller, D. B.; Schultz, J. In PLoS ONE, 8(7), bl. e69945. 2013.
  • {{T}he bilaterian roots of cordon-bleu}. Schultz, J.; Terhoeven, N. In BMC Res Notes, 6(1), bl. 393. 2013.
2012[ to top ]
  • {{I}{T}{S}2 database {I}{V}: interactive taxon sampling for internal transcribed spacer 2 based phylogenies}. Koetschan, C.; Hackl, T.; Muller, T.; Wolf, M.; Forster, F.; Schultz, J. In Mol. Phylogenet. Evol., 63(3), ble. 585–588. 2012.
  • {{T}he protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms}. 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. In Mol. Cell Proteomics, 11(11), ble. 1306–1319. 2012.
  • {{T}he {I}{T}{S}2 {D}atabase}. Merget, B.; Koetschan, C.; Hackl, T.; Forster, F.; Dandekar, T.; Muller, T.; Schultz, J.; Wolf, M. In J Vis Exp, (61). 2012.
  • Morpheme networks reveal language dynamics. Keller, Daniela Barbara; Schultz, Jörg. In Actes des 11es Journées Internationales d’Analyse Statistique des Données Textuelles / Proceedings of the 11th International Conference on the Statistical Analysis of Textual Data. 2012.
2010[ to top ]
  • {{I}ncluding {R}{N}{A} secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees}. Keller, A.; Forster, F.; Muller, T.; Dandekar, T.; Schultz, J.; Wolf, M. In Biol. Direct, 5, bl. 4. 2010.
  • {{E}volutionary distances in the twilight zone--a rational kernel approach}. Schwarz, R. F.; Fletcher, W.; Forster, F.; Merget, B.; Wolf, M.; Schultz, J.; Markowetz, F. In PLoS ONE, 5, bl. e15788. 2010.
  • {{T}he {I}{T}{S}2 {D}atabase {I}{I}{I}--sequences and structures for phylogeny}. Koetschan, C.; Forster, F.; Keller, A.; Schleicher, T.; Ruderisch, B.; Schwarz, R.; Muller, T.; Wolf, M.; Schultz, J. In Nucleic Acids Res., 38, ble. D275–279. 2010.
  • {{P}rotein interaction networks--more than mere modules}. Pinkert, S.; Schultz, J.; Reichardt, J. In PLoS Comput. Biol., 6, bl. e1000659. 2010.
2009[ to top ]
  • {{A} kinome of 2600 in the ciliate {P}aramecium tetraurelia}. Bemm, F.; Schwarz, R.; Forster, F.; Schultz, J. In FEBS Lett., 583, ble. 3589–3592. 2009.
  • {{W}hen one plus one equals three: biochemistry and bioinformatics combine to answer complex questions}. Kroiss, M.; Fischer, U.; Schultz, J. In Fly (Austin), 3, ble. 210–212. 2009.
  • {5.8{S}-28{S} r{R}{N}{A} interaction and {H}{M}{M}-based {I}{T}{S}2 annotation}. Keller, A.; Schleicher, T.; Schultz, J.; Muller, T.; Dandekar, T.; Wolf, M. In Gene, 430, ble. 50–57. 2009.
  • {{I}{T}{S}2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics}. Schultz, J.; Wolf, M. In Mol. Phylogenet. Evol., 52, ble. 520–523. 2009.
  • {{D}etecting species-site dependencies in large multiple sequence alignments}. Schwarz, R.; Seibel, P. N.; Rahmann, S.; Schoen, C.; Huenerberg, M.; Muller-Reible, C.; Dandekar, T.; Karchin, R.; Schultz, J.; Muller, T. In Nucleic Acids Res., 37, ble. 5959–5968. 2009.
  • {{P}ositive selection in tick saliva proteins of the {S}alp15 family}. Schwalie, P. C.; Schultz, J. In J. Mol. Evol., 68, ble. 186–191. 2009.
  • {{E}volutionary flexibility of protein complexes}. Seidl, M. F.; Schultz, J. In BMC Evol. Biol., 9, bl. 155. 2009.
  • {{P}artially-supervised protein subclass discovery with simultaneous annotation of functional residues}. Georgi, B.; Schultz, J.; Schliep, A. In BMC Struct. Biol., 9, bl. 68. 2009.
2008[ to top ]
  • {{T}he {I}{T}{S}2 {D}atabase {I}{I}: homology modelling {R}{N}{A} structure for molecular systematics}. Selig, C.; Wolf, M.; Muller, T.; Dandekar, T.; Schultz, J. In Nucleic Acids Res., 36, ble. D377–380. 2008.
  • {{P}rof{D}ist{S}: (profile-) distance based phylogeny on sequence--structure alignments}. Wolf, M.; Ruderisch, B.; Dandekar, T.; Schultz, J.; Muller, T. In Bioinformatics, 24, ble. 2401–2402. 2008.
  • {{E}xplorative data analysis of {M}{C}{L} reveals gene expression networks implicated in survival and prognosis supported by explorative {C}{G}{H} analysis}. Blenk, S.; Engelmann, J. C.; Pinkert, S.; Weniger, M.; Schultz, J.; Rosenwald, A.; Muller-Hermelink, H. K.; Muller, T.; Dandekar, T. In BMC Cancer, 8, bl. 106. 2008.
  • {{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}. Perotti, C.; Liu, R.; Parusel, C. T.; Bocher, N.; Schultz, J.; Bork, P.; Pfitzner, E.; Groner, B.; Shemanko, C. S. In Breast Cancer Res., 10, bl. R94. 2008.
  • {{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}. Kroiss, M.; Schultz, J.; Wiesner, J.; Chari, A.; Sickmann, A.; Fischer, U. In Proc. Natl. Acad. Sci. U.S.A., 105, ble. 10045–10050. 2008.
2007[ to top ]
  • {{G}enome {E}xpression {P}athway {A}nalysis {T}ool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context}. Weniger, M.; Engelmann, J. C.; Schultz, J. In BMC Bioinformatics, 8, bl. 179. 2007.
  • {{D}istinguishing species}. Muller, T.; Philippi, N.; Dandekar, T.; Schultz, J.; Wolf, M. In RNA, 13, ble. 1469–1472. 2007.
  • {{E}xonization of active mouse {L}1s: a driver of transcriptome evolution?}. Zemojtel, T.; Penzkofer, T.; Schultz, J.; Dandekar, T.; Badge, R.; Vingron, M. In BMC Genomics, 8, bl. 392. 2007.
  • {{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}. Blenk, S.; Engelmann, J.; Weniger, M.; Schultz, J.; Dittrich, M.; Rosenwald, A.; Muller-Hermelink, H. K.; Muller, T.; Dandekar, T. In Cancer Inform, 3, ble. 399–420. 2007.
2006[ to top ]
  • {{A}nalysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets}. 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. In Nat. Genet., 38, ble. 285–293. 2006.
  • {4{S}{A}{L}{E}--a tool for synchronous {R}{N}{A} sequence and secondary structure alignment and editing}. Seibel, P. N.; Muller, T.; Dandekar, T.; Schultz, J.; Wolf, M. In BMC Bioinformatics, 7, bl. 498. 2006.
  • {{T}he internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses}. Schultz, J.; Muller, T.; Achtziger, M.; Seibel, P. N.; Dandekar, T.; Wolf, M. In Nucleic Acids Res., 34, ble. W704–707. 2006.
  • {{M}odelling interaction sites in protein domains with interaction profile hidden {M}arkov models}. Friedrich, T.; Pils, B.; Dandekar, T.; Schultz, J.; Muller, T. In Bioinformatics, 22, ble. 2851–2857. 2006.
  • {{S}{M}{A}{R}{T} 5: domains in the context of genomes and networks}. Letunic, I.; Copley, R. R.; Pils, B.; Pinkert, S.; Schultz, J.; Bork, P. In Nucleic Acids Res., 34, ble. D257–260. 2006.
2005[ to top ]
  • {{H}omology modeling revealed more than 20,000 r{R}{N}{A} internal transcribed spacer 2 ({I}{T}{S}2) secondary structures}. Wolf, M.; Achtziger, M.; Schultz, J.; Dandekar, T.; Muller, T. In RNA, 11, ble. 1616–1623. 2005.
  • {{V}ariation in structural location and amino acid conservation of functional sites in protein domain families}. Pils, B.; Copley, R. R.; Schultz, J. In BMC Bioinformatics, 6, bl. 210. 2005.
  • {{A} common core of secondary structure of the internal transcribed spacer 2 ({I}{T}{S}2) throughout the {E}ukaryota}. Schultz, J.; Maisel, S.; Gerlach, D.; Muller, T.; Wolf, M. In RNA, 11, ble. 361–364. 2005.
  • {{S}tructural genomics of human proteins--target selection and generation of a public catalogue of expression clones}. Bussow, K.; Scheich, C.; Sievert, V.; Harttig, U.; Schultz, J.; Simon, B.; Bork, P.; Lehrach, H.; Heinemann, U. In Microb. Cell Fact., 4, bl. 21. 2005.
2004[ to top ]
  • {{H}{T}{T}{M}, a horizontally transferred transmembrane domain}. Schultz, J. In Trends Biochem. Sci., 29, ble. 4–7. 2004.
  • {{A} novel conserved family of nitric oxide synthase?}. Zemojtel, T.; Penzkofer, T.; Dandekar, T.; Schultz, J. In Trends Biochem. Sci., 29, ble. 224–226. 2004.
  • {{S}{M}{A}{R}{T} 4.0: towards genomic data integration}. Letunic, I.; Copley, R. R.; Schmidt, S.; Ciccarelli, F. D.; Doerks, T.; Schultz, J.; Ponting, C. P.; Bork, P. In Nucleic Acids Res., 32, ble. D142–144. 2004.
  • {{E}volution of the multifunctional protein tyrosine phosphatase family}. Pils, B.; Schultz, J. In Mol. Biol. Evol., 21, ble. 625–631. 2004.
  • {{H}{M}{M} {L}ogos for visualization of protein families}. Schuster-Bockler, B.; Schultz, J.; Rahmann, S. In BMC Bioinformatics, 5, bl. 7. 2004.
  • {{I}nactive enzyme-homologues find new function in regulatory processes}. Pils, B.; Schultz, J. In J. Mol. Biol., 340, ble. 399–404. 2004.
2002[ to top ]
  • {{P}redicting protein cellular localization using a domain projection method}. Mott, R.; Schultz, J.; Bork, P.; Ponting, C. P. In Genome Res., 12, ble. 1168–1174. 2002.
  • {{G}enome expression analysis of {A}nopheles gambiae: responses to injury, bacterial challenge, and malaria infection}. Dimopoulos, G.; Christophides, G. K.; Meister, S.; Schultz, J.; White, K. P.; Barillas-Mury, C.; Kafatos, F. C. In Proc. Natl. Acad. Sci. U.S.A., 99, ble. 8814–8819. 2002.
  • {{S}ystematic identification of novel protein domain families associated with nuclear functions}. Doerks, T.; Copley, R. R.; Schultz, J.; Ponting, C. P.; Bork, P. In Genome Res., 12, ble. 47–56. 2002.
  • {{P}rediction of structure and functional residues for {O}-{G}lc{N}{A}case, a divergent homologue of acetyltransferases}. Schultz, J.; Pils, B. In FEBS Lett., 529, ble. 179–182. 2002.
  • {{I}nitial sequencing and comparative analysis of the mouse genome}. 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. Von; 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. In Nature, 420, ble. 520–562. 2002.
  • {{F}unctional organization of the yeast proteome by systematic analysis of protein complexes}. 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. In Nature, 415, ble. 141–147. 2002.
  • {{S}equence analysis of multidomain proteins: past perspectives and future directions}. Copley, R. R.; Ponting, C. P.; Schultz, J.; Bork, P. In Adv. Protein Chem., 61, ble. 75–98. 2002.
  • {{R}ecent improvements to the {S}{M}{A}{R}{T} domain-based sequence annotation resource}. Letunic, I.; Goodstadt, L.; Dickens, N. J.; Doerks, T.; Schultz, J.; Mott, R.; Ciccarelli, F.; Copley, R. R.; Ponting, C. P.; Bork, P. In Nucleic Acids Res., 30, ble. 242–244. 2002.
2001[ to top ]
  • {{I}nitial sequencing and analysis of the human genome}. 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. In Nature, 409, ble. 860–921. 2001.
  • {{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]}. Schultz, J.; Jones, T.; Bork, P.; Sheer, D.; Blencke, S.; Steyrer, S.; Wellbrock, U.; Bevec, D.; Ullrich, A.; Wallasch, C. In Genomics, 71, ble. 368–370. 2001.
2000[ to top ]
  • {{S}{M}{A}{R}{T}: a web-based tool for the study of genetically mobile domains}. Schultz, J.; Copley, R. R.; Doerks, T.; Ponting, C. P.; Bork, P. In Nucleic Acids Res., 28, ble. 231–234. 2000.
  • {{E}volution of domain families}. Ponting, C. P.; Schultz, J.; Copley, R. R.; Andrade, M. A.; Bork, P. In Adv. Protein Chem., 54, ble. 185–244. 2000.
  • {{A}nopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines}. 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. In Proc. Natl. Acad. Sci. U.S.A., 97, ble. 6619–6624. 2000.
  • {{M}ore than 1,000 putative new human signalling proteins revealed by {E}{S}{T} data mining}. Schultz, J.; Doerks, T.; Ponting, C. P.; Copley, R. R.; Bork, P. In Nat. Genet., 25, ble. 201–204. 2000.
1999[ to top ]
  • {{N}o {S}ec7-homology domain in guanine-nucleotide-exchange factors that act on {R}as and {R}ho}. Ponting, C. P.; Bork, P.; Schultz, J.; Aravind, L. In Trends Biochem. Sci., 24, ble. 177–178. 1999.
  • {{E}ukaryotic signalling domain homologues in archaea and bacteria. {A}ncient ancestry and horizontal gene transfer}. Ponting, C. P.; Aravind, L.; Schultz, J.; Bork, P.; Koonin, E. V. In J. Mol. Biol., 289, ble. 729–745. 1999.
  • {{P}rotein families in multicellular organisms}. Copley, R. R.; Schultz, J.; Ponting, C. P.; Bork, P. In Curr. Opin. Struct. Biol., 9, ble. 408–415. 1999.
  • {{S}{M}{A}{R}{T}: identification and annotation of domains from signalling and extracellular protein sequences}. Ponting, C. P.; Schultz, J.; Milpetz, F.; Bork, P. In Nucleic Acids Res., 27, ble. 229–232. 1999.
1998[ to top ]
  • {{S}{M}{A}{R}{T}, a simple modular architecture research tool: identification of signaling domains}. Schultz, J.; Milpetz, F.; Bork, P.; Ponting, C. P. In Proc. Natl. Acad. Sci. U.S.A., 95, ble. 5857–5864. 1998.
1997[ to top ]
  • {{S}{P}{R}{Y} domains in ryanodine receptors ({C}a(2+)-release channels)}. Ponting, C.; Schultz, J.; Bork, P. In Trends Biochem. Sci., 22, ble. 193–194. 1997.
  • {{S}ecreted fringe-like signaling molecules may be glycosyltransferases}. Yuan, Y. P.; Schultz, J.; Mlodzik, M.; Bork, P. In Cell, 88, ble. 9–11. 1997.
  • {{S}{A}{M} as a protein interaction domain involved in developmental regulation}. Schultz, J.; Ponting, C. P.; Hofmann, K.; Bork, P. In Protein Sci., 6, ble. 249–253. 1997.
  • {{C}ytoplasmic signalling domains: the next generation}. Bork, P.; Schultz, J.; Ponting, C. P. In Trends Biochem. Sci., 22, ble. 296–298. 1997.
1996[ to top ]
  • {{T}he protein phosphatase 2{C} ({P}{P}2{C}) superfamily: detection of bacterial homologues}. Bork, P.; Brown, N. P.; Hegyi, H.; Schultz, J. In Protein Sci., 5, ble. 1421–1425. 1996.