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Staff at EMBL

Aidan Budd

Senior Project Manager Bioinformatics
Gibson Team

EMBL Heidelberg, Meyerhofstra├če 1, 69117 Heidelberg, Germany

E-mail: send a mail
Web page: http://www.embl-heidelberg.de/~budd/

Publications

The eukaryotic linear motif resource ELM: 10 years and counting. Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., Speck, T., Kruger, D., Grebnev, G., Kuban, M., Strumillo, M., Uyar, B., Budd, A., Altenberg, B., Seiler, M., Chemes, L.B., Glavina, J., Sanchez, I.E., Diella, F. & Gibson, T.J. Nucleic Acids Res. 2014 Jan;42(Database issue):D259-66. doi: 10.1093/nar/gkt1047.Epub 2013 Nov 7. Europe PMC

Best practices in bioinformatics training for life scientists. Via, A., Blicher, T., Bongcam-Rudloff, E., Brazas, M.D., Brooksbank, C., Budd, A., De Las Rivas, J., Dreyer, J., Fernandes, P.L., van Gelder, C., Jacob, J., Jimenez, R.C., Loveland, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Schneider, M.V. & Attwood, T.K. Brief Bioinform. 2013 Sep;14(5):528-37. doi: 10.1093/bib/bbt043. Epub 2013 Jun25. Europe PMC

iAnn: an event sharing platform for the life sciences. Jimenez, R.C., Albar, J.P., Bhak, J., Blatter, M.C., Blicher, T., Brazas, M.D., Brooksbank, C., Budd, A., De Las Rivas, J., Dreyer, J., van Driel, M.A., Dunn, M.J., Fernandes, P.L., van Gelder, C.W., Hermjakob, H., Ioannidis, V., Judge, D.P., Kahlem, P., Korpelainen, E., Kraus, H.J., Loveland, J., Mayer, C., McDowall, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Salazar, G.A., Schneider, R., Via, A., Villaveces, J.M., Yu, P., Schneider, M.V., Attwood, T.K. & Corpas, M. Bioinformatics. 2013 Aug 1;29(15):1919-21. doi: 10.1093/bioinformatics/btt306.Epub 2013 Jun 5. Europe PMC

Biggest challenges in bioinformatics. Fuller, J.C., Khoueiry, P., Dinkel, H., Forslund, K., Stamatakis, A., Barry, J., Budd, A., Soldatos, T.G., Linssen, K. & Rajput, A.M. EMBO Rep. 2013 Mar 15. doi: 10.1038/embor.2013.34. Europe PMC

Evaluating the Evolutionary Origins of Unexpected Character Distributions within the Bacterial Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum. Budd, A. & Devos, D.P. Front Microbiol. 2012;3:401. doi: 10.3389/fmicb.2012.00401. Epub 2012 Nov 23. Europe PMC

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. Schneider, M.V., Walter, P., Blatter, M.C., Watson, J., Brazas, M.D., Rother, K., Budd, A., Via, A., van Gelder, C.W., Jacob, J., Fernandes, P., Nyronen, T.H., De Las Rivas, J., Blicher, T., Jimenez, R.C., Loveland, J., McDowall, J., Jones, P., Vaughan, B.W., Lopez, R., Attwood, T.K. & Brooksbank, C. Brief Bioinform. 2012 May;13(3):383-9. doi: 10.1093/bib/bbr064. Epub 2011 Nov 22. Europe PMC

Attributes of short linear motifs. Davey, N.E., Van Roey, K., Weatheritt, R.J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H. & Gibson, T.J. Mol Biosyst. 2012 Jan;8(1):268-81. doi: 10.1039/c1mb05231d. Epub 2011 Sep 12. Europe PMC

ELM--the database of eukaryotic linear motifs. Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A., Jodicke, L., Dammert, M.A., Schroeter, C., Hammer, M., Schmidt, T., Jehl, P., McGuigan, C., Dymecka, M., Chica, C., Luck, K., Via, A., Chatr-Aryamontri, A., Haslam, N., Grebnev, G., Edwards, R.J., Steinmetz, M.O., Meiselbach, H., Diella, F. & Gibson, T.J. Nucleic Acids Res. 2012 Jan 1;40(D1):D242-D251. Epub 2011 Nov 21. Europe PMC

Introduction to genome biology: features, processes, and structures. Budd, A. Methods Mol Biol. 2012;855:3-49. Europe PMC

Diversity of genome organisation. Budd, A. Methods Mol Biol. 2012;855:51-76. Europe PMC

Characterization of a regulatory unit that controls melanization and affects longevity of mosquitoes. An, C., Budd, A., Kanost, M.R. & Michel, K. Cell Mol Life Sci. 2011 Jun;68(11):1929-39. doi: 10.1007/s00018-010-0543-z. Epub2010 Oct 17. Europe PMC

Basic Molecular Evolution Workshop - A trans-African virtual training course: "Virtual Workshops": Is Africa ready to embrace the concept? Ommeh, S., Budd, A., Ngara, M.V., Njaci, I. & de Villiers, E.P. Bioessays. 2011 Apr;33(4):243-7. doi: 10.1002/bies.201000139. Epub 2011Feb 11. Europe PMC

Structure-function analysis of hRPC62 provides insights into RNA polymerase III transcription initiation. Lefevre, S., Dumay-Odelot, H., El-Ayoubi, L., Budd, A., Legrand, P., Pinaud, N., Teichmann, M. & Fribourg, S. Nat Struct Mol Biol. 2011 Mar;18(3):352-8. Epub 2011 Feb 27. Europe PMC

Bioinformatics training: a review of challenges, actions and support requirements. Schneider, M.V., Watson, J., Attwood, T., Rother, K., Budd, A., McDowall, J., Via, A., Fernandes, P., Nyronen, T., Blicher, T., Jones, P., Blatter, M.C., De Las Rivas, J., Judge, D.P., van der Gool, W. & Brooksbank, C. Brief Bioinform. 2010 Nov;11(6):544-51. doi: 10.1093/bib/bbq021. Epub 2010 Jun18. Europe PMC

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. Croset, V., Rytz, R., Cummins, S.F., Budd, A., Brawand, D., Kaessmann, H., Gibson, T.J. & Benton, R. PLoS Genet. 2010 Aug 19;6(8). pii: e1001064. Europe PMC

Characterization of drCol 15a1b: a novel component of the stem cell niche in the zebrafish retina. Gonzalez-Nunez, V., Nocco, V. & Budd, A. Stem Cells. 2010 Aug;28(8):1399-411. doi: 10.1002/stem.461. Europe PMC

The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins. Santarella-Mellwig, R., Franke, J., Jaedicke, A., Gorjanacz, M., Bauer, U., Budd, A., Mattaj, I.W. & Devos, D.P. PLoS Biol. 2010 Jan 19;8(1):e1000281. Europe PMC

ELM: the status of the 2010 eukaryotic linear motif resource. Gould, C.M., Diella, F., Via, A., Puntervoll, P., Gemund, C., Chabanis-Davidson, S., Michael, S., Sayadi, A., Bryne, J.C., Chica, C., Seiler, M., Davey, N.E., Haslam, N., Weatheritt, R.J., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave, G., Aasland, R., Helmer-Citterich, M., Linding, R. & Gibson, T.J. Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016.Epub 2009 Nov 17. Europe PMC

Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure. Batisse, J., Batisse, C., Budd, A., Bottcher, B. & Hurt, E. J Biol Chem. 2009 Dec 11;284(50):34911-7. Epub 2009 Oct 19. Europe PMC

Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences. Ettwiller, L., Budd, A., Spitz, F. & Wittbrodt, J. Genome Biol. 2008 Dec 16;9(12):R172. Europe PMC

The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila. Deddouche, S., Matt, N., Budd, A., Mueller, S., Kemp, C., Galiana-Arnoux, D., Dostert, C., Antoniewski, C., Hoffmann, J.A. & Imler, J.L. Nat Immunol. 2008 Dec;9(12):1425-32. Epub 2008 Oct 26. Europe PMC

Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Trave, G. & Gibson, T.J. Front Biosci. 2008 May 1;13:6580-603. Europe PMC

An immune-responsive serpin, SRPN6, mediates mosquito defense against malaria parasites. Abraham, E.G., Pinto, S.B., Ghosh, A., Vanlandingham, D.L., Budd, A., Higgs, S., Kafatos, F.C., Jacobs-Lorena, M. & Michel, K. Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16327-32. Epub 2005 Oct 31. Europe PMC

Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei. Michel, K., Budd, A., Pinto, S., Gibson, T.J. & Kafatos, F.C. EMBO Rep 2005 Sep;6(9):891-7. Europe PMC

Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? Budd, A., Blandin, S., Levashina, E.A. & Gibson, T.J. Genome Biol 2004;5(6):R38. Epub 2004 May 26. Europe PMC

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases. Bimpikis, K., Budd, A., Linding, R. & Gibson, T.J. Nucleic Acids Res 2003 Jul 1;31(13):3792-4. Europe PMC

RPA is an initiation factor for human chromosomal DNA replication. Szuts, D., Kitching, L., Christov, C., Budd, A., Peak-Chew, S. & Krude, T. Nucleic Acids Res. 2003 Mar 15;31(6):1725-34. Europe PMC