Publications and Presentations

Martin G. Reese

2006

Reese MG and Guigo R, (2006). ``EGASP: Introduction.'', Genome Biol. 7(Suppl 1):S1, 2006.
O 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.
O Paper(PDF)

2005

Guigo, R. and Reese, M.G., (2005). ``EGASP: collaboration through competition to find human genes.'', Nat Methods, 2(8):575-7, 2005.
O Paper(PDF)

2003

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.
O Paper(PDF)

2002

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.


2001

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.
O Paper(PDF)

2000

Ph.D. Thesis

O 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.
O 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.
O 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.
O 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.

1999

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).
O 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.
O 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.
O Abstract
O 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]
O Abstract

1998

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.
O Abstract
O 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]
O Abstract

1997

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.
O Abstract
O 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.
O Abstract
O Paper (Postscript, approximately 280 KB or compressed version RECOMB97.ps.gz 66 KB).
O 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.
O Abstract
O Paper (PDF).


1996

Harris, N.L., Reese, M.G., and Eeckman, F.H. (1996). ``Genotater: A workbench for sequence annotation'' Eighth International Genome Sequencing and Analysis Conference, Hilton Head, SC. [Talk]

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.
O Abstract
O Paper (PDF).
O 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]
O 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]
O Abstract
O 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.
O Abstract
O 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]
O Abstract

1995

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.
O Abstract
O 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.
O Abstract

1994

Reese, M.G., Reczko, M., Bohr, H. and Suhai, S. (1994). ``Prediction of E.Coli Promoter Sites Utilizing the Transcription Geometry with Time Delay Neural Networks'', internal report at the German Cancer Research Center.
O Abstract


Diploma Thesis

(sorry, but the Thesis are in German)

Title: Erkennung von Promotoren in pro- und eukaryontischen DNA-Sequenzen durch künstliche Neuronale Netze

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

O Read abstract.
O If you really want to, you can down load the whole thesis (pdf) O (Postscript, approximately 13 MB). A compressed version (1.8 MB) is also available.


Last modified: Mon Aug 28 16:19:54 PDT 2006
reese@alum.calberkeley.org