Reese MG and
Guigo R, (2006).
``EGASP: Introduction.'',
Genome Biol. 7(Suppl 1):S1, 2006.
Paper(PDF)
Guigo R, Flicek P,Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S,
Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C,
Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG, (2006).
``EGASP: the human ENCODE Genome Annotation Assessment Project.'',
Genome Biol. 7(Suppl 1):S2, 2006.
Paper(PDF)
Guigo, R. and Reese, M.G., (2005).
``EGASP: collaboration through competition to find human genes.'',
Nat Methods, 2(8):575-7, 2005.
Paper(PDF)
Jannot, A-S., Essioux, L., Reese, M.G., Clerget-Darpoux, F., (2003).
``Improved use of SNP information to detect the role of genes.'',
Genet Epidemiol, 25(2):158-67, 2003.
Paper(PDF)
Jannot, A-S., Essioux, L., Reese, M.G., Clerget-Darpoux, F., (2002).
``Improved use of SNP information to detect the role of genes.'',
Am Soc Hum Gen, Baltimore, 2002.
Reese, M.G.,
(2001).
``Application of a time-delay neural network
to promoter annotation in the Drosophila melanogaster genome'',
Comput Chem, 26(1):51-6, 2001.
Paper(PDF)
Thesis(PDF)
Title: Computational prediction of gene structure and regulation in the genome of Drosophila melanogaster
Authors: Reese, M.G.
Supervisor: Gerry M. Rubin, UC Berkeley, Anette Preiss, University of Hohenheim, Germany.
Location: Berkeley Drosophila Genome Project
Date: May 2000
Reese, M.G., (2000). ``Application of a time-delay neural network to the annotation of the Drosophila melanogaster genome'', Proceedings of the 2000 Convention of the Society for the Study of Artificial Intelligence and the Simulation of Behaviour: Artifical Intelligence in Bioinformatics edited by A.C.R. Martin and D. Corne.
Lewis, S.E., Ashburner, M. and Reese, M.G., (2000).
``Annotating eukaryote genomes.''
Current Opinion in Structural Biology, 10(3):349-354, 2000.
Paper(PDF)
Reese, M.G.,
Kulp, D., Tammana, H., Haussler, D., (2000).
``Genie - Gene finding in Drosophila melanogaster.''
Genome Research, 10(4):529-538, 2000.
Paper (PDF)
Reese, M.G.,
Hartzell, G., Harris, N.L., Ohler, U., Abril,
J.F. and Lewis S.E., (2000).
``Genome Annotation Assessment in Drosophila melanogaster.''
Genome Research, 10(4):483-501, 2000.
Paper (PDF)
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides
PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE,
Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell
MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M,
Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor
Miklos GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin
D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson
KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan
MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H,
Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C,
Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew
I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC,
Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann
W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A,
Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D,
Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ,
Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA,
Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z,
Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei
B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV,
Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L,
Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR,
Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V,
Reese MG,
Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC,
Siden-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC,
Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter
E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach
J, Williams SM, Woodage T, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh
RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN,
Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM,
Venter JC, (2000) ``The Genome Sequence of Drosophila
melanogaster.''
Science, 287(5461):2185-2196, 2000.
Reese, M.G., and
Harris, N.L.,
Hartzell, G. and Lewis, S.E. (1999).
``The challenge of annotating a complete eukaryotic genome: A case
study in Drosophila melanogaster'',
Tutorial at
the International Conference on Intelligent
Systems for Molecular Biology '99 (ISMB), Heidelberg, Germany, August
6-10, 1999. The tutorial discussed the Genome
Annotation Assessment
Project 1 (GASP1).
On-line handouts
Reese, M.G.,
Harris, N.L.,
Hartzell, G. and Lewis, S.E. (1999).
``The Drosophila melanogaster annotation experiment``,
HUGO (Human Genome Organization) meeting on the ``Annotation of
function in genomes'', EMBL, Heidelberg, Germany, organized by
Peer Bork, August 1999.
Ashburner, M., Misra, S., Roote, J., Blazej, R., Davis, T., Doyle, C.,
Galle, R., George, R., Harris, N., Hartzell, G., Harvey, D., Hong, L.,
Houston, K., Hoskins, R., Johnson, G., Martin, C., Moshrefi, A.,
Palazzolo, M.,
Reese,
M.G., Spradling, A., Tsang, G., Wan, K., Whitelaw, K.,
Kimmel, B., Celniker, S. and Rubin, G.M..
(1999).
``An exploration of the sequence of a 2.9-megabase region of the
genome of drosophila melanogaster. The adh region.'',
Genetics, Vol. 153, 179-219, 1999.
Paper (PDF)
Ohler,
U., Harbeck S., Niemann H., Noeth, E. and
Reese, M.G.(1999).
``Interpolated Markov Chains for Eukaryotic Promoter Recognition'',
Bioinformatics,Vol. 15 Issue 5, 362-369, 1999.
Abstract
Paper (PDF)
Friese, E.,
Reese, M.G.
and Rubin, G.M. (1999).
``ORFFinder, a program to detect open reading frames, frameshifts and
startcodons in Drosophila melanogaster cDNA's'',
Proceedings of the
Third Annual International Conference on Computational
Molecular Biology (RECOMB), 1999, Lyon, France,
edited by S. Istrail, R. Karp, T. Lengauer, P. Pevzner, R. Shamir and
M. Waterman. [Poster]
Abstract
Ohler,
U. and
Reese, M.G.(1998).
``Detection of eukaryotic promoter regions using polygrams'', In R. Hofestädt, Editor, Molekulare
Bioinformatik, p. 89-100, Aachen, 1998. Shaker.
Abstract
Paper (Postscript)
Harris, N.L.,
Pfeiffer, B.D.,
Reese, M.G., and
Celniker, S.E. (1998).
``Large-scale annotation with Genotator and Genie'',
Biocomputing:
Proceedings of the 1998 Pacific Symposium edited by
R. B. Altman, A. K. Dunker, L. Hunter and T. E. Klein, World
Scientific, New York. [Poster]
Abstract
Reese, M.G. and Kulp, D. (1997). ``Integration of neural networks for gene features into a hidden Markov model based genefinder'', Workshop on "Statistical analysis of DNA and Protein Sequences", Isaac Newton Institute for Mathematical Sciences, University of Cambridge.
Reese, M.G.,
Eeckman, F.H.,
Kulp, D., Haussler, D. (1997).
``Improved Splice Site Detection in Genie'',
J. Comp. Biol., Vol. 4 Issue 3, 311-323, 1997.
Abstract
Paper (PDF)
Reese, M.G.,
Eeckman, F.H.,
Kulp, D., Haussler, D. (1997).
``Improved Splice Site Detection in Genie'',
Proceedings of the
First Annual International Conference on Computational
Molecular Biology (RECOMB), 1997, Santa Fe, New Mexico,
edited by M. Waterman, ACM Press, New York.
Abstract
Paper (Postscript,
approximately 280 KB or compressed version
RECOMB97.ps.gz 66 KB).
Slide Presentation (PDF-Format
approximatley 2 MB or compressed version
recomb97.pdf.gz 1.3 MB).
Kulp, D., Haussler, D.,
Reese, M.G., and
Eeckman, F.H.
(1997).
``Integrating Database Homology in a Probabilistic Gene Structure Model'',
Biocomputing: Proceedings of the 1997 Pacific Symposium edited by R. B. Altman, A. K. Dunker, L. Hunter and T. E. Klein, World Scientific, New York, 232-244.
Abstract
Paper (PDF).
Kulp, D., Haussler, D.,
Reese, M.G., and
Eeckman, F.H.
(1996).
``A generalized hidden Markov model for the
recognition of human genes in DNA'',
Proc. Conf. on Intelligent
Systems for Molecular Biology '96 edited by D.J.States, P. Agarwal,
T. Gaasterland, L. Hunter and R. Smith, 134-142,
St. Louis, Missouri, AAAI/MIT Press.
Abstract
Paper (PDF).
Try out our gene finding program
Genie!
Harris, N.L.,
Reese, M.G., and
Eeckman, F.H.
(1996).
``Towards Automatic Recognition of Exons'',
Intelligent Systems for Molecular Biology '96,
St. Louis, Missouri. [Poster]
Abstract
Reese, M.G., and
Eeckman, F.H.
(1996).
``Splice Sites: A detailed neural network study'',
Proceedings of the 1996
Genome Mapping & Sequencing Meeting, Cold Spring Harbour, New York, arranged by D. Bentley, E. Green and P. Hieter. [Poster]
Abstract
Try out our
splice site prediction program!
Reese, M.G.,
Lund, O., Bohr, J., Bohr, H., Hansen, J.E., and Brunak, S. (1996).
``Distance distributions in proteins: A six parameter representation'',
Protein Engineering,
Vol. 9 No. 7.
Abstract
Paper (Postscript,
approximately 370 KB or compressed version di-paper.ps.gz 85 KB).
Reese, M.G.,
Harris, N.L., and
Eeckman, F.H.
(1996).
``Large Scale Sequencing Specific Neural Networks for
Promoter and Splice Site Recognition'',
Biocomputing: Proceedings of the 1996 Pacific Symposium edited by Lawrence
Hunter and Teri E. Klein, World Scientific Publishing Co, Singapore, 737-738 [Poster]
Abstract
Reese, M.G., and
Eeckman, F.H.
(1995).
``Novel Neural Network Prediction Systems for Human Promoters
and Splice Sites'',
Proceedings of the
Workshop on Gene-Finding and Gene Structure PredictionPennsylvania, Philadelphia,
edited by D. Searls, J. Fickett, G. Stormo and M. Noordewier.
Abstract
Paper (Postscript,
approximately 180 KB or compressed version gf-paper.ps.gz 33 KB).
Reese, M.G., and
Eeckman, F.H.
(1995).
``New Neural Network Algorithms for Improved Eukaryotic Promoter Site
Recognition'',
Genome Science and Technology,
Vol. 1 No. 1: p.45,
Proceedings of the
The seventh international Genome sequencing and analysis conference,
Hilton Head Island, South Carolina, edited by J.C. Venter and D. Doyle.
Abstract
Abstract
Authors: Reese, M.G.
Supervisor: Reczko ,M., Suhai, S., Schlegel, S..
Location: Division of Molecular Biophysics at the German Cancer Research Center
Date: April 1994
Read abstract.
If you really want to, you can down load the whole
thesis (pdf)
(Postscript, approximately 13 MB). A compressed
version (1.8 MB) is also available.