EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

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Publications

Total: 32 publication(s)

2015

Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, Blomberg N. (2015)

A quick guide for building a successful bioinformatics community.

PLoS Comput. Biol. 11(2) doi:10.1371/journal.pcbi.1003972
Europe PMC | doi

Budd A, Dinkel H, Corpas M, Fuller JC, Rubinat L, Devos DP, Khoueiry PH, Förstner KU, Georgatos F, Rowland F, Sharan M, Binder JX, Grace T, Traphagen K, Gristwood A, Wood NT. (2015)

Ten simple rules for organizing an unconference.

PLoS Comput. Biol. 11(1) doi:10.1371/journal.pcbi.1003905
Europe PMC | doi

Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV, Attwood TK. (2015)

The GOBLET Training Portal: A Global Repository of Bioinformatics Training Materials, Courses and Trainers

Bioinformatics 31(1):140-142. doi:10.1093/bioinformatics/btu601
Europe PMC | doi


2014

Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. (2014)

Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation.

Chem. Rev. 114(13):6733-6778. doi:10.1021/cr400585q
Europe PMC | doi

Budd A, Stamatakis A. (2014)

Phylogeny-related terms.

In: Hancock JM, Zvelebil MJ (eds.), Concise Encyclopaedia of Bioinformatics and Computational Biology. 2nd edn. Wiley-Blackwell.

Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, Chemes LB, Glavina J, Sánchez IE, Diella F, Gibson TJ. (2014)

The eukaryotic linear motif resource ELM: 10 years and counting

Nucleic Acids Res. 42(Database issue):D259-66. doi:10.1093/nar/gkt1047
Europe PMC | doi


2013

Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK. (2013)

Best practices in bioinformatics training for life scientists

Brief. Bioinformatics 14(5):528-537. doi:10.1093/bib/bbt043
Europe PMC | doi

Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M. (2013)

iAnn: an event sharing platform for the life sciences

Bioinformatics 29(15):1919-1921. doi:10.1093/bioinformatics/btt306
Europe PMC | doi

Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM, HUB Participants. (2013)

Biggest challenges in bioinformatics

EMBO Rep. 14(4):302-304. doi:10.1038/embor.2013.34
Europe PMC | doi


2012

Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C. (2012)

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Brief. Bioinformatics 13(3):383-389. doi:10.1093/bib/bbr064
Europe PMC | doi

Budd A. (2012)

Diversity of genome organisation

Methods Mol. Biol. 855:51-76. doi:10.1007/978-1-61779-582-4_2
Europe PMC | doi

Budd A. (2012)

Introduction to genome biology: features, processes, and structures

Methods Mol. Biol. 855:3-49. doi:10.1007/978-1-61779-582-4_1
Europe PMC | doi

Budd A, Devos DP. (2012)

Evaluating the Evolutionary Origins of Unexpected Character Distributions within the Bacterial Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum

Front Microbiol 3:401. doi:10.3389/fmicb.2012.00401
Europe PMC | doi

Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ. (2012)

Attributes of short linear motifs

Mol Biosyst 8(1):268-281. doi:10.1039/c1mb05231d
Europe PMC | doi

Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, 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 RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ. (2012)

ELM--the database of eukaryotic linear motifs

Nucleic Acids Res. 40(Database issue):D242-51. doi:10.1093/nar/gkr1064
Europe PMC | doi


2011

An C, Budd A, Kanost MR, Michel K. (2011)

Characterization of a regulatory unit that controls melanization and affects longevity of mosquitoes

Cell. Mol. Life Sci. 68(11):1929-1939. doi:10.1007/s00018-010-0543-z
Europe PMC | doi

Ommeh S, Budd A, Ngara MV, Njaci I, de Villiers EP. (2011)

Basic Molecular Evolution Workshop--A trans-African virtual training course: "Virtual Workshops": Is Africa ready to embrace the concept?

Bioessays 33(4):243-247. doi:10.1002/bies.201000139
Europe PMC | doi

Lefèvre S, Dumay-Odelot H, El-Ayoubi L, Budd A, Legrand P, Pinaud N, Teichmann M, Fribourg S. (2011)

Structure-function analysis of hRPC62 provides insights into RNA polymerase III transcription initiation

Nat. Struct. Mol. Biol. 18(3):352-358. doi:10.1038/nsmb.1996
Europe PMC | doi


2010

Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Judge DP, van der Gool W, Brooksbank C. (2010)

Bioinformatics training: a review of challenges, actions and support requirements

Brief. Bioinformatics 11(6):544-551. doi:10.1093/bib/bbq021
Europe PMC | doi

Croset V, Rytz R, Cummins SF, Budd A, Brawand D, Kaessmann H, Gibson TJ, Benton R. (2010)

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction

PLoS Genet. 6(8):e1001064. doi:10.1371/journal.pgen.1001064
Europe PMC | doi

Gonzalez-Nunez V, Nocco V, Budd A. (2010)

Characterization of drCol 15a1b: a novel component of the stem cell niche in the zebrafish retina

Stem Cells 28(8):1399-1411. doi:10.1002/stem.461
Europe PMC | doi

Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ. (2010)

ELM: the status of the 2010 eukaryotic linear motif resource

Nucleic Acids Res. 38(Database issue):D167-80. doi:10.1093/nar/gkp1016
Europe PMC | doi

Santarella-Mellwig R, Franke J, Jaedicke A, Gorjanacz M, Bauer U, Budd A, Mattaj IW, Devos DP. (2010)

The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins

PLoS Biol. 8(1):e1000281. doi:10.1371/journal.pbio.1000281
Europe PMC | doi


2009

Batisse J, Batisse C, Budd A, Böttcher B, Hurt E. (2009)

Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure

J. Biol. Chem. 284(50):34911-34917. doi:10.1074/jbc.m109.062034
Europe PMC | doi


2008

Deddouche S, Matt N, Budd A, Mueller S, Kemp C, Galiana-Arnoux D, Dostert C, Antoniewski C, Hoffmann JA, Imler JL. (2008)

The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila

Nat. Immunol. 9(12):1425-1432. doi:10.1038/ni.1664
Europe PMC | doi

Diella F, Haslam N, Chica C, Budd A, Michael S, Brown NP, Trave G, Gibson TJ. (2008)

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

Front. Biosci. 13:6580-6603. doi:10.2741/3175
Europe PMC | doi

Ettwiller L, Budd A, Spitz F, Wittbrodt J. (2008)

Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences

Genome Biol. 9(12):R172. doi:10.1186/gb-2008-9-12-r172
Europe PMC | doi


2005

Abraham EG, Pinto SB, Ghosh A, Vanlandingham DL, Budd A, Higgs S, Kafatos FC, Jacobs-Lorena M, Michel K. (2005)

An immune-responsive serpin, SRPN6, mediates mosquito defense against malaria parasites

Proc. Natl. Acad. Sci. U.S.A. 102(45):16327-16332. doi:10.1073/pnas.0508335102
Europe PMC | doi

Michel K, Budd A, Pinto S, Gibson TJ, Kafatos FC. (2005)

Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei

EMBO Rep. 6(9):891-897. doi:10.1038/sj.embor.7400478
Europe PMC | doi


2004

Budd A, Blandin S, Levashina EA, Gibson TJ. (2004)

Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?

Genome Biol. 5(6):R38. doi:10.1186/gb-2004-5-6-r38
Europe PMC | doi


2003

Bimpikis K, Budd A, Linding R, Gibson TJ. (2003)

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases

Nucleic Acids Res. 31(13):3792-3794. doi:10.1093/nar/gkg535
Europe PMC | doi

Szüts D, Kitching L, Christov C, Budd A, Peak-Chew S, Krude T. (2003)

RPA is an initiation factor for human chromosomal DNA replication

Nucleic Acids Res. 31(6):1725-1734. doi:10.1093/nar/gkg269
Europe PMC | doi