Martin Madera
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Background
- MSc in Theoretical & Experimental Physics, Trinity College, Cambridge
- PhD in Molecular Biology from the MRC Laboratory of Molecular Biology, Cambridge
- Postdoctoral fellow at the European Bioinformatics Institute, Hinxton, Cambridge
- Postdoctoral scholar in the Department of Biomolecular Engineering, University California, Santa Cruz
Current projects
Publications
- Wilson D., Pethica R., Zhou Y., Talbot C., Vogel C.,
Madera M., Chothia C. and Gough J. (2009)
SUPERFAMILY-sophisticated comparative genomics, data mining,
visualization and phylogeny. Nucl. Acids Res. 37, D380-D386.
PDF
- Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A.,
Binns D., Bork P., Das U., Daugherty L., Duquenne L., Finn R.D.,
Gough J., Haft D., Hulo N., Kahn D., Kelly E., Laugraud A.,
Letunic I., Lonsdale D., Lopez R., Madera M., Maslen J.,
McAnulla C., McDowell J., Mistry J., Mitchell A., Mulder N.,
Natale D., Orengo C., Quinn A.F., Selengut J.D., Sigrist C.J.A.,
Thimma M., Thomas P.D., Valentin F., Wilson D., Wu C.H. and
Yeats C.
(2009). InterPro: the integrative protein signature
database. Nucl. Acids Res. 37, D211-D215.
PDF
- Madera M. (2008) Profile Comparer: a program for scoring
and aligning profile hidden Markov models. Bioinformatics 24,
2630-2631.
PDF
- Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A.,
Binns D., Bork P., Buillard V., Cerutti L., Copley R., Courcelle E.,
Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J.,
Haft D., Hulo N., Hunter S., Kahn D., Kanapin A., Kejariwal A.,
Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic
I., Madera M., Maslen J., McAnulla C., McDowall J., Mistry J.,
Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R.,
Selengut J.D., Sigrist C.J. A., Thomas P.D., Valentin F., Wilson D.,
Wu C.H., Yeats C.
(2007) New developments in the InterPro database. Nucl. Acids
Res. 35, D224-28.
PDF
- Wilson D., Madera M., Vogel C., Chothia C., Gough J. (2007)
The SUPERFAMILY database in 2007: families and
functions. Nucl. Acids Res. 35, D308-13.
PDF
- Babu M. M., Priya M. L., Selvan A. T., Madera M., Gough
J. and Sankaran K. (2006). A database of bacterial lipoproteins
(DOLOP) with functional assignments to predicted lipoproteins. J
Bacteriol. 188, 2761-73.
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Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
Bajic V.B., Brenner S.E., Batalov S., Forrest A.R.R., Zavolan M.,
Davis M.J., Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato
A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L.,
Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V.,
Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple
B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom
P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M.,
Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori
T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K.,
Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A.,
Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J.,
Kitamura H., Kitano H., Kollias G., Krishnan S.P.T., Kruger A.,
Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich
L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M.,
Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake
S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H.,
Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O.,
Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G.,
Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M.,
Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Sekiguchi
C.Schoenbach, K., Semple C.A.M., Seno S., Sessa L., Sheng Y., Shibata
Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka
E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan
S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van
Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky
E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D.,
Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume
D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M.,
Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T.,
Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno
H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata
K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
(2005). The Transcriptional Landscape of the Mammalian
Genome. Science 309, 1559-63.
PDF
- Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.-A.,
Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q.,
Tunggal B., Kummerfeld S., Madera M., B. Konfortov A., Rivero F.,
Bankier A.T., Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P.,
Pilcher K., Chen G., Saunders D., Sodergren E., Davis P.,
Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N.,
Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.,
Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I.,
Muzny D., Mourier T., Pain A., Lu M., Harper D., Lindsay R.,
Hauser H., James K., Quiles M., Madan Babu M., Saito T.,
Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
Knights A., Loulseged H., Mungall K., Oliver K., Price C., Quail M.A.,
Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
Ma J., Kohara Y., Sharp S., Simmonds M., Spiegler S., Tivey A.,
Sugano S., White B., Walker D., Woodward J., Winckler T., Tanaka Y.,
Shaulsky G., Schleicher M., Weinstock G., Rosenthal A., Cox E.C.,
Chisholm R.L., Gibbs R., Loomis W.F., Platzer M., Kay R.R.,
Williams J., Dear P.H., Noegel A.A., Barrell B., and Kuspa A.
(2005) The genome of the social amoeba Dictyostelium discoideum.
Nature 435, 43-57.
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- Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns
D., Bradley P., Bork P., Bucher P., Cerutti L., Copley R., Courcelle
E., Das U., Durbin R., Fleischmann W., Gough J., Haft D., Harte N.,
Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lonsdale D., Lopez R.,
Letunic I., Madera M., Maslen J., McDowall J., Mitchell A., Nikolskaya
A.N., Orchard S., Pagni M., Ponting C.P., Quevillon E., Selengut J.,
Sigrist C.J. A., Silventoinen V., Studholme D.J., Vaughan R., Wu
C.H. (2005) InterPro, progress and status in 2005. Nucl. Acids
Res. 33, D201-5.
PDF
- de Bono B., Madera M. and Chothia C. (2004) VH gene
segments in the mouse and human genomes.
J. Mol. Biol. 342, 131-43.
PDF
- Kummerfeld S.K., Vogel C., Madera M., Pacold M. and
Teichmann S.A. (2004) Evolution of multi-domain proteins by gene
fusion and fission. Intel. Syst. Mol. Biol. (ISMB) 2004.
PDF
- Madera M., Vogel C., Kummerfeld S.K., Chothia C. and Gough
J. (2004) The SUPERFAMILY database in 2004: additions and
improvements. Nucl. Acids Res. 32, D235-9.
PDF
- Bankier A.T., Spriggs H.F., Fartmann B., Konfortov B.A., Madera
M., Vogel C., Teichmann S.A., Ivens A. and Dear P.H. (2003)
Integrated mapping, chromosomal sequencing and sequence analysis of
Cryptosporidium parvum. Genome Res. 13, 1787-99.
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- Madera M. and Gough J. (2002). A comparison of hidden Markov model procedures for remote homology detection. Nucl. Acids Res. 30, 4321-8. PDF