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1. OMICS AND PROGNSTIC MARKERS

Author

K. Adachi, H. Sasaki, S. Nagahisa, K. Yoshida, N. Hattori, Y. Nishiyama, T. Kawase, M. Hasegawa, M. Abe, Y. Hirose, A. Alentorn, Y. Marie, S. Poggioli, H. Alshehhi, B. Boisselier, C. Carpentier, K. Mokhtari, L. Capelle, D. Figarella-Branger, K. Hoang-Xuan, M. Sanson, J.-Y. Delattre, A. Idbaih, S. Yust-Katz, M. Anderson, A. Olar, A. Eterovic, N. Ezzeddine, K. Chen, H. Zhao, G. Fuller, K. Aldape, J. de Groot, N. Andor, J. Harness, S. G. Lopez, T. L. Fung, H. W. Mewes, C. Petritsch, A. Arivazhagan, K. Somasundaram, K. Thennarasu, P. Pandey, B. Anandh, V. Santosh, B. Chandramouli, A. Hegde, P. Kondaiah, M. Rao, R. Bell, R. Kang, C. Hong, J. Song, J. Costello, R. Nagarajan, B. Zhang, A. Diaz, T. Wang, L. Bie, Y. Li, H. Liu, W. F. C. Luyo, M. H. Carnero, M. E. P. Iruegas, A. R. Morell, M. C. Figueiras, R. L. Lopez, C. F. Valverde, A. K.-Y. Chan, J. C.-S. Pang, N. Y.-F. Chung, K. K.-W. Li, W. S. Poon, D. T.-M. Chan, Y. Wang, H.-a. K. Ng, M. Chaumeil, P. Larson, H. Yoshihara, D. Vigneron, S. Nelson, R. Pieper, J. Phillips, S. Ronen, V. Clark, Z. E. Omay, A. Serin, J. Gunel, B. Omay, C. Grady, M. Youngblood, K. Bilguvar, J. Baehring, J. Piepmeier, P. Gutin, A. Vortmeyer, C. Brennan, M. N. Pamir, T. Kilic, B. Krischek, M. Simon, K. Yasuno, M. Gunel, A. L. Cohen, M. Sato, K. D. Aldape, C. Mason, K. Diefes, L. Heathcock, L. Abegglen, D. Shrieve, W. Couldwell, J. D. Schiffman, H. Colman, Q. G. D'Alessandris, T. Cenci, M. Martini, L. Ricci-Vitiani, R. De Maria, L. M. Larocca, R. Pallini, B. Theeler, F. Lang, G. Rao, M. Gilbert, E. Sulman, R. Luthra, K. Eterovic, M. Routbort, R. Verhaak, G. Mills, J. Mendelsohn, F. Meric-Bernstam, A. Yung, K. MacArthur, S. Hahn, G. Kao, R. Lustig, M. Alonso-Basanta, S. Chandrasekaran, E. P. Wileyto, E. Reyes, J. Dorsey, K. Fujii, K. Kurozumi, T. Ichikawa, M. Onishi, J. Ishida, Y. Shimazu, B. Kaur, E. A. Chiocca, I. Date, C. Geisenberger, A. Mock, R. Warta, C. Schwager, C. Hartmann, A. von Deimling, A. Abdollahi, C. Herold-Mende, O. Gevaert, A. Achrol, S. Gholamin, S. Mitra, E. Westbroek, J. Loya, L. Mitchell, S. Chang, G. Steinberg, S. Plevritis, S. Cheshier, J. Xu, S. Napel, G. Zaharchuk, G. Harsh, D. Gutman, C. Holder, R. Colen, W. Dunn, R. Jain, L. Cooper, S. Hwang, A. Flanders, D. Brat, J. Hayes, A. Droop, H. Thygesen, M. Boissinot, D. Westhead, S. Short, S. Lawler, P. Bady, S. Kurscheid, M. Delorenzi, M. E. Hegi, C. Crosby, C. Faulkner, T. Smye-Rumsby, K. Kurian, M. Williams, K. Hopkins, A. Palmer, H. Williams, C. Wragg, H. R. Haynes, K. M. Kurian, P. White, T. Oka, L. Jalbert, A. Elkhaled, R. Jensen, K. Salzman, M. Schabel, D. Gillespie, M. Mumert, B. Johnson, T. Mazor, M. Barnes, S. Yamamoto, H. Ueda, K. Tatsuno, K. Aihara, A. Bollen, M. Hirst, M. Marra, A. Mukasa, N. Saito, H. Aburatani, M. Berger, B. Taylor, S. Popov, A. Mackay, W. Ingram, A. Burford, A. Jury, M. Vinci, C. Jones, D. T. W. Jones, V. Hovestadt, S. Picelli, W. Wang, P. A. Northcott, M. Kool, G. Reifenberger, T. Pietsch, M. Sultan, H. Lehrach, M.-L. Yaspo, A. Borkhardt, P. Landgraf, R. Eils, A. Korshunov, M. Zapatka, B. Radlwimmer, S. M. Pfister, P. Lichter, A. Joy, I. Smirnov, M. Reiser, W. Shapiro, S. Kim, B. Feuerstein, C. Jungk, S. Friauf, A. Unterberg, T. A. Juratli, J. McElroy, W. Meng, A. Huebner, K. D. Geiger, D. Krex, G. Schackert, A. Chakravarti, T. Lautenschlaeger, B. Y. Kim, W. Jiang, J. Beiko, S. Prabhu, F. DeMonte, R. Sawaya, D. Cahill, I. McCutcheon, C. Lau, L. Wang, K. Terashima, S. Yamaguchi, M. Burstein, J. Sun, T. Suzuki, R. Nishikawa, H. Nakamura, A. Natsume, S. Terasaka, H.-K. Ng, D. Muzny, R. Gibbs, D. Wheeler, X.-q. Zhang, S. Sun, K.-f. Lam, K. M. Y. Kiang, J. K. S. Pu, A. S. W. Ho, G. K. K. Leung, F. Loebel, W. T. Curry, F. G. Barker, N. Lelic, A. S. Chi, D. P. Cahill, D. Lu, J. Yin, C. Teo, K. McDonald, A. Madhankumar, C. Weston, B. Slagle-Webb, J. Sheehan, A. Patel, M. Glantz, J. Connor, C. Maire, J. Francis, C.-Z. Zhang, J. Jung, V. Manzo, V. Adalsteinsson, H. Homer, B. Blumenstiel, C. S. Pedamallu, E. Nickerson, A. Ligon, C. Love, M. Meyerson, K. Ligon, L. E. Jalbert, S. J. Nelson, A. W. Bollen, I. V. Smirnov, J. S. Song, A. B. Olshen, M. S. Berger, S. M. Chang, B. S. Taylor, J. F. Costello, S. Mehta, B. Armstrong, S. Peng, A. Bapat, M. Berens, B. Melendez, M. Mollejo, P. Mur, T. Hernandez-Iglesias, C. Fiano, J. Ruiz, J. A. Rey, V. Stadler, A. Schulte, K. Lamszus, C. Schichor, M. Westphal, J.-C. Tonn, O. Morozova, S. Katzman, M. Grifford, S. Salama, D. Haussler, A. Olshen, S. Fouse, S. Nakamizo, T. Sasayama, H. Tanaka, K. Tanaka, K. Mizukawa, M. Yoshida, E. Kohmura, P. Northcott, D. Jones, S. Pfister, R. Otani, S. Takayanagi, K. Saito, S. Tanaka, M. Shin, T. Ozawa, M. Riester, Y.-K. Cheng, J. Huse, K. Helmy, N. Charles, M. Squatrito, F. Michor, E. Holland, M. Perrech, L. Dreher, G. Rohn, R. Goldbrunner, M. Timmer, B. Pollo, V. Palumbo, C. Calatozzolo, M. Patane, R. Nunziata, M. Farinotti, A. Silvani, S. Lodrini, G. Finocchiaro, E. Lopez, A. Rioscovian, R. Ruiz, G. Siordia, A. P. de Leon, C. Rostomily, R. Rostomily, D. Silbergeld, D. Kolstoe, M. Chamberlain, J. Silber, P. Roth, A. Keller, J. Hoheisel, P. Codo, A. Bauer, C. Backes, P. Leidinger, E. Meese, E. Thiel, A. Korfel, M. Weller, G. Nagae, M. Nagane, J. Z. Sanborn, T. Mikkelsen, S. Jhanwar, L. Chin, M. Nishihara, M. Schliesser, C. Grimm, E. Weiss, R. Claus, D. Weichenhan, M. Weiler, T. Hielscher, F. Sahm, B. Wiestler, A.-C. Klein, J. Blaes, C. Plass, W. Wick, G. Stragliotto, A. Rahbar, C. Soderberg-Naucler, M. Won, R. Ezhilarasan, P. Sun, D. Blumenthal, M. Vogelbaum, R. Jenkins, R. Jeraj, P. Brown, K. Jaeckle, D. Schiff, J. Dignam, J. Atkins, D. Brachman, M. Werner-Wasik, M. Mehta, J. Shen, J. Luan, A. Yu, M. Matsutani, Y. Liang, T.-K. Man, A. Trister, M. Tokita, S. Mikheeva, A. Mikheev, S. Friend, M. van den Bent, L. Erdem, T. Gorlia, M. Taphoorn, J. Kros, P. Wesseling, H. Dubbink, A. Ibdaih, P. French, H. van Thuijl, J. Heimans, B. Ylstra, J. Reijneveld, A. Prabowo, I. Scheinin, H. van Essen, W. Spliet, C. Ferrier, P. van Rijen, T. Veersema, M. Thom, A. S.-v. Meeteren, E. Aronica, H. Kim, S. Zheng, D. J. Brat, S. Virk, S. Amini, C. Sougnez, J. Barnholtz-Sloan, R. G. W. Verhaak, C. Watts, A. Sottoriva, I. Spiteri, S. Piccirillo, A. Touloumis, P. Collins, J. Marioni, C. Curtis, S. Tavare, B. Tews, T. P. C. Yeung, B. Al-Khazraji, L. Morrison, L. Hoffman, D. Jackson, T.-Y. Lee, S. Yartsev, G. Bauman, J. Fu, R. Vegesna, Y. Mao, L. E. Heathcock, W. Torres-Garcia, S. Wang, A. McKenna, C. W. Brennan, W. K. A. Yung, J. N. Weinstein, E. P. Sulman, and D. Koul

Subjects
Abstracts, Cancer Research, Text mining, Oncology, business.industry, Neurology (clinical), Computational biology, Biology, Omics, business
Published
2013

2. Bioinformatics and Genome Analysis

Author

H.-W. Mewes, H. Seidel, B. Weiss, H.-W. Mewes, H. Seidel, and B. Weiss

Subjects
Biochemistry, Bioinformatics, Medical genetics
Published
2013

3. Functional modules by relating protein interaction networks and gene expression

Author

H. W. Mewes and Sabine Tornow

Subjects
Macromolecular Substances, Genes, Fungal, Gene regulatory network, Gene Expression, Computational biology, Biology, Fungal Proteins, Correlation, Open Reading Frames, Interaction network, Gene Expression Regulation, Fungal, Yeasts, Databases, Genetic, Genetics, Probability, Fungal protein, Cell Cycle, Fungal genetics, Computational Biology, Articles, Gene expression profiling, Probability distribution, Algorithms, Biological network, Protein Binding, Statistical Distributions
Abstract

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships.

Published
2003

4. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana

Author

null The EU Arabidopsis Genome Project, M. Bevan, I. Bancroft, E. Bent, K. Love, H. Goodman, C. Dean, R. Bergkamp, W. Dirkse, M. Van Staveren, W. Stiekema, L. Drost, P. Ridley, S.-A. Hudson, K. Patel, G. Murphy, P. Piffanelli, H. Wedler, E. Wedler, R. Wambutt, T. Weitzenegger, T. M. Pohl, N. Terryn, J. Gielen, R. Villarroel, R. De Clerck, M. Van Montagu, A. Lecharny, S. Auborg, I. Gy, M. Kreis, N. Lao, T. Kavanagh, S. Hempel, P. Kotter, K.-D. Entian, M. Rieger, M. Schaeffer, B. Funk, S. Mueller-Auer, M. Silvey, R. James, A. Montfort, A. Pons, P. Puigdomenech, A. Douka, E. Voukelatou, D. Milioni, P. Hatzopoulos, E. Piravandi, B. Obermaier, H. Hilbert, A. Düsterhöft, T. Moores, J. D. G. Jones, T. Eneva, K. Palme, V. Benes, S. Rechman, W. Ansorge, R. Cooke, C. Berger, M. Delseny, M. Voet, G. Volckaert, H.-W. Mewes, S. Klosterman, C. Schueller, and N. Chalwatzis

Subjects
Yeast artificial chromosome, Genetics, Multidisciplinary, Gene map, Arabidopsis, Chromosome Mapping, Locus (genetics), Sequence Analysis, DNA, Genome project, Human artificial chromosome, Biology, Genes, Plant, Chromosome 4, Multigene Family, Chromosome 19, Chromosome 21, Chromosomes, Artificial, Yeast, Genome, Plant, Plant Proteins
Abstract

The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.

Published
1998

5. Pharmacopsychiatry. Editorial

Author

F, Tretter, O, Pogarell, D, Rujescu, E, Meisenzahl, and H W, Mewes

Subjects
Psychiatry, Mental Disorders, Systems Biology, Humans, Models, Psychological
Published
2012

6. Complete DNA sequence of yeast chromosome II

Author

H, Feldmann, M, Aigle, G, Aljinovic, B, André, M C, Baclet, C, Barthe, A, Baur, A M, Bécam, N, Biteau, E, Boles, T, Brandt, M, Brendel, M, Brückner, F, Bussereau, C, Christiansen, R, Contreras, M, Crouzet, C, Cziepluch, N, Démolis, T, Delaveau, F, Doignon, H, Domdey, S, Düsterhus, E, Dubois, B, Dujon, M, El Bakkoury, K D, Entian, M, Feurmann, W, Fiers, G M, Fobo, C, Fritz, H, Gassenhuber, N, Glandsdorff, A, Goffeau, L A, Grivell, M, de Haan, C, Hein, C J, Herbert, C P, Hollenberg, K, Holmstrøm, C, Jacq, M, Jacquet, J C, Jauniaux, J L, Jonniaux, T, Kallesøe, P, Kiesau, L, Kirchrath, P, Kötter, S, Korol, S, Liebl, M, Logghe, A J, Lohan, E J, Louis, Z Y, Li, M J, Maat, L, Mallet, G, Mannhaupt, F, Messenguy, T, Miosga, F, Molemans, S, Müller, F, Nasr, B, Obermaier, J, Perea, A, Piérard, E, Piravandi, F M, Pohl, T M, Pohl, S, Potier, M, Proft, B, Purnelle, M, Ramezani Rad, M, Rieger, M, Rose, I, Schaaff-Gerstenschläger, B, Scherens, C, Schwarzlose, J, Skala, P P, Slonimski, P H, Smits, J L, Souciet, H Y, Steensma, R, Stucka, A, Urrestarazu, Q J, van der Aart, L, van Dyck, A, Vassarotti, I, Vetter, F, Vierendeels, S, Vissers, G, Wagner, P, de Wergifosse, K H, Wolfe, M, Zagulski, F K, Zimmermann, H W, Mewes, and K, Kleine

Subjects
Quality Control, Genes, Fungal, Molecular Sequence Data, Saccharomyces cerevisiae, Biology, General Biochemistry, Genetics and Molecular Biology, Open Reading Frames, Chromosome 15, Chromosome 16, Chromosome 19, Cloning, Molecular, DNA, Fungal, Molecular Biology, Repetitive Sequences, Nucleic Acid, Genetics, Base Composition, Base Sequence, Sequence Homology, Amino Acid, General Immunology and Microbiology, General Neuroscience, Chromosome Mapping, Reproducibility of Results, Sequence Analysis, DNA, Telomere, Cosmids, Chromosome 17 (human), Chromosome 4, Chromosome 3, Chromosomes, Fungal, Chromosome 21, Chromosome 22, Research Article
Abstract

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Published
1994

7. Affective disorders as complex dynamic diseases--a perspective from systems biology

Author

Christoph W. Turck, Felix Tretter, Peter J. Gebicke-Haerter, Dan Rujescu, U. an der Heiden, and H. W. Mewes

Subjects
State variable, Hydrocortisone, Systems biology, Context (language use), Models, Biological, Empirical research, Neurobiology, Dummy variable, Humans, Pharmacology (medical), Computer Simulation, Disease, Simple (philosophy), Cognitive science, Depressive Disorder, Depression, Mood Disorders, Mental Disorders, Systems Biology, Perspective (graphical), Brain, General Medicine, Neuropsychiatry, Psychiatry and Mental health, Molecular network, Nonlinear Dynamics, Psychology, Neuroscience, Signal Transduction
Abstract

Understanding mental disorders and their neurobiological basis encompasses the conceptual management of "complexity" and "dynamics". For example, affective disorders exhibit several fluctuating state variables on psychological and biological levels and data collected of these systems levels suggest quasi-chaotic periodicity leading to use concepts and tools of the mathematics of nonlinear dynamic systems. Regarding this, we demonstrate that the concept of "Dynamic Diseases" could be a fruitful way for theory and empirical research in neuropsychiatry. In a first step, as an example, we focus on the analysis of dynamic cortisol regulation that is important for understanding depressive disorders. In this case, our message is that extremely complex phenomena of a disease may be explained as resulting from perplexingly simple nonlinear interactions of a very small number of variables. Additionally, we propose that and how widely used complex circuit diagrams representing the macroanatomic structures and connectivities of the brain involved in major depression or other mental disorders may be "animated" by quantification, even by using expert-based estimations (dummy variables). This method of modeling allows to develop exploratory computer-based numerical models that encompass the option to explore the system by computer simulations (in-silico experiments). Also inter- and intracellular molecular networks involved in affective disorders could be modeled by this procedure. We want to stimulate future research in this theoretical context.

Published
2011

8. Pharmacopsychiatry. Editorial

Author

F, Tretter, D, Rujescu, C W, Turck, and H W, Mewes

Subjects
Mood Disorders, Psychopharmacology, Systems Biology, Humans
Published
2011

11. Bioinformatics and Genome Analysis

Author

B. Weiss, H. Seidel, and H.-W. Mewes

Subjects
chemistry.chemical_compound, Glycosylation, chemistry, Membrane protein, Gene expression, Graph (abstract data type), Biology, Bioinformatics, Proteomics, Genome, Protein secondary structure, Gene
Abstract

1 Dissecting the Genetic Component of Complex Diseases in Humans.- 2 Bioinformatics of Membrane Proteins.- 3 SNAPping Up Functionally Related Genes Based on Context Information: A Colinearity-Free Approach.- 4 Promoter Analysis.- 5 Cluster Analysis and Its Applications to Gene Expression Data.- 6 Statistical Methods for Analyzing Gene Expression Data for Cancer Research.- 7 Comparing Secondary Structure 'Stick' Models of Proteins Using Graph Matching with Double Dynamic Programming.- 8 Computational Structural Proteomics.- 9 Proteomics in Biological Research: The Challenge to Make Proteins Speak.- 10 Construction and Prediction of Protein-Protein Interaction Maps.- 11 Bioinformatics, Cellular Flows, and Calculation.- 12 Graph-Based Analysis of Metabolic Networks.- 13 Orphan Protein Function and Its Relation to Glycosylation.- Previous Volumes Published in This Series.

Published
2002

12. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana

Author

S, Tabata, T, Kaneko, Y, Nakamura, H, Kotani, T, Kato, E, Asamizu, N, Miyajima, S, Sasamoto, T, Kimura, T, Hosouchi, K, Kawashima, M, Kohara, M, Matsumoto, A, Matsuno, A, Muraki, S, Nakayama, N, Nakazaki, K, Naruo, S, Okumura, S, Shinpo, C, Takeuchi, T, Wada, A, Watanabe, M, Yamada, M, Yasuda, S, Sato, M, de la Bastide, E, Huang, L, Spiegel, L, Gnoj, A, O'Shaughnessy, R, Preston, K, Habermann, J, Murray, D, Johnson, T, Rohlfing, J, Nelson, T, Stoneking, K, Pepin, J, Spieth, M, Sekhon, J, Armstrong, M, Becker, E, Belter, H, Cordum, M, Cordes, L, Courtney, W, Courtney, M, Dante, H, Du, J, Edwards, J, Fryman, B, Haakensen, E, Lamar, P, Latreille, S, Leonard, R, Meyer, E, Mulvaney, P, Ozersky, A, Riley, C, Strowmatt, C, Wagner-McPherson, A, Wollam, M, Yoakum, M, Bell, N, Dedhia, L, Parnell, R, Shah, M, Rodriguez, L H, See, D, Vil, J, Baker, K, Kirchoff, K, Toth, L, King, A, Bahret, B, Miller, M, Marra, R, Martienssen, W R, McCombie, R K, Wilson, G, Murphy, I, Bancroft, G, Volckaert, R, Wambutt, A, Düsterhöft, W, Stiekema, T, Pohl, K D, Entian, N, Terryn, N, Hartley, E, Bent, S, Johnson, S A, Langham, B, McCullagh, J, Robben, B, Grymonprez, W, Zimmermann, U, Ramsperger, H, Wedler, K, Balke, E, Wedler, S, Peters, M, van Staveren, W, Dirkse, P, Mooijman, R K, Lankhorst, T, Weitzenegger, G, Bothe, M, Rose, J, Hauf, S, Berneiser, S, Hempel, M, Feldpausch, S, Lamberth, R, Villarroel, J, Gielen, W, Ardiles, O, Bents, K, Lemcke, G, Kolesov, K, Mayer, S, Rudd, H, Schoof, C, Schueller, P, Zaccaria, H W, Mewes, M, Bevan, P, Fransz, and Synthetic Systems Biology (SILS, FNWI)

Subjects
Genetics, Whole genome sequencing, Genome evolution, Multidisciplinary, DNA, Plant, biology, Sequence analysis, Arabidopsis, Chromosome Mapping, Chromosome, Sequence Analysis, DNA, biology.organism_classification, Genome, Complete sequence, Plant Research International, Centromere, Animals, Humans, Life Science, Genome, Plant, Plant Proteins
Abstract

The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.

Published
2000

13. Integrative analysis of protein interaction data

Author

M, Fellenberg, K, Albermann, A, Zollner, H W, Mewes, and J, Hani

Subjects
Proteome, RNA Splicing, Statistics as Topic, Animals, Humans, Proteins, Protein Binding
Abstract

We have developed a method for the integrative analysis of protein interaction data. It comprises clustering, visualization and data integration components. The method is generally applicable for all sequenced organisms. Here, we describe in detail the combination of protein interaction data in the yeast Saccharomyces cerevisiae with the functional classification of all yeast proteins. We evaluate the utility of the method by comparison with experimental data and deduce hypotheses about the functional role of so far uncharacterized proteins. Further applications of the integrative analysis method are discussed. The method presented here is powerful and flexible. We show that it is capable of mining large-scale data sets.

Published
2000

14. Clearing a path through the jungle: progress in Arabidopsis genomics

Author

M, Bevan, I, Bancroft, H W, Mewes, R, Martienssen, and R, McCombie

Subjects
Arabidopsis, Chromosome Mapping, Sequence Analysis, DNA, Chromosomes, Genome, Plant
Abstract

Progress in sequencing the genome of the model plant Arabidopsis is reviewed. The resulting analysis of the sequence indicates an information-rich genome that is being tackled by a variety of high-throughput approaches aimed at understanding the functions of plant genes. The information derived from these systematic studies is providing important new knowledge of biological processes found uniquely in plants for comparison with that obtained in other multicellular organisms.

Published
1999

15. MIPS: a database for genomes and protein sequences

Author

H. W. Mewes, K. Heumann, A. Kaps, K. Mayer, F. Pfeiffer, S. Stocker, and D. Frishman

Subjects
Expressed Sequence Tags, Genome, Databases, Factual, Genome, Human, Arabidopsis, Information Storage and Retrieval, Proteins, Germany, Multigene Family, Yeasts, Genetics, Animals, Humans, Amino Acid Sequence, Genome, Fungal, Genome, Plant, Research Article
Abstract

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database.

Published
1998

16. Systems Biology of Oscillatory Processes in Sleep and Mental Disorders

Author

H. W. Mewes, E. M. Meisenzahl, Felix Tretter, Oliver Pogarell, and Dan Rujescu

Subjects
Cognitive science, Psychiatry and Mental health, Biological Clocks, Mental Disorders, Systems Biology, Systems biology, Humans, Pharmacology (medical), General Medicine, Sleep, Psychology, Sleep in non-human animals, Developmental psychology
Published
2013

17. A top-down approach to whole genome visualization

Author

K, Heumann, C, Harris, and H W, Mewes

Subjects
Computer Communication Networks, Open Reading Frames, Human Genome Project, Humans, Chromosomes, Fungal, Software
Abstract

The investigation of large DNA contigs like complete chromosomes or genomes requires novel methods of data visualization. The complex information contained in a genome, particularly the relation of its individual genetic elements, needs to be accessible in a comprehensive, intelligent and intelligible manner. The yeast genome is expected to contain more than 6,000 Open Reading Frames (ORFs). As yet, the function of many of these ORFs has not been characterized satisfactorily. Also, many ORFs are found to have redundant copies elsewhere in the genome that originated from common ancestors. Other genetic elements (e.g. Tss, delta-elements, t-RNAs) are present in multiple copies. To visualize these relationships, a top-down "genome browser" is introduced that enables inspection of genomic data at different levels of abstraction (e.g. chromosomes, coding/non-coding regions, high/low levels of similarity). This novel tool is a key component for the integrated services approach to biological sequence data management (Heumann et al. 1995) and is accessible through the world wide web (WWW). This work demonstrates how the genome browser visualizes the results of an all-against-all comparison of the elements in the yeast genome as a graph. Interactive navigational queries across yeast chromosomes along the lines of sequence similarity open versatile options for the detailed investigation of genome properties. For sequence comparison the hashed position tree HPT (MewesHeumann 1995) is applied. Sequence similarity relationships are represented using the genome similarity graph (GSG) (HeumannMewes 1996c).

Published
1996

18. Editorial

Author

F. Tretter, D. Rujescu, C. W. Turck, and H. W. Mewes

Subjects
Psychiatry and Mental health, Pharmacology (medical), General Medicine
Published
2011

20. The Yeast Genome Directory

Author

A. Goffeau, R. Aert, M. L. Agostini-Carbone, A. Ahmed, M. Aigle, L. Alberghina, K. Albermann, M. Albers, M. Aldea, D. Alexandraki, G. Aljinovic, E. Allen, J. Alt-Mörbe, B. André, S. Andrews, W. Ansorge, G. Antoine, R. Anwar, A. Aparicio, R. Araujo, J. Arino, F. Arnold, J. Arroyo, E. Aviles, U. Backes, M. C. Baclet, K. Badcock, A. Bahr, V. Baladron, J. P. G. Ballesta, A. T. Bankier, A. Banrevi, M. Bargues, L. Baron, T. Barreiros, B. G. Barrell, C. Barthe, A. B. Barton, A. Baur, A.-M. Bécam, A. Becker, I. Becker, J. Beinhauer, V. Benes, P. Benit, G. Berben, E. Bergantino, P. Bergez, A. Berno, I. Bertani, N. Biteau, A. J. Bjourson, H. Blöcker, C. Blugeon, C. Bohn, E. Boles, P. A. Bolle, M. Bolotin-Fukuhara, R. Bordonné, J. Boskovic, P. Bossier, D. Botstein, G. Bou, S. Bowman, J. Boyer, P. Brandt, T. Brandt, M. Brendel, T. Brennan, R. Brinkman, A. Brown, A. J. P. Brown, D. Brown, M. Brückner, C. V. Bruschi, J. M. Buhler, M. J. Buitrago, F. Bussereau, H. Bussey, A. Camasses, C. Carcano, G. Carignani, J. Carpenter, A. Casamayor, C. Casas, L. Castagnoli, H. Cederberg, E. Cerdan, N. Chalwatzis, R. Chanet, E. Chen, G. Chéret, J. M. Cherry, T. Chillingworth, C. Christiansen, J.-C. Chuat, E. Chung, C. Churcher, C. M. Churcher, M. W. Clark, M. L. Clemente, A. Coblenz, M. Coglievina, E. Coissac, L. Colleaux, R. Connor, R. Contreras, J. Cooper, T. Copsey, F. Coster, R. Coster, J. Couch, M. Crouzet, C. Cziepluch, B. Daignan-Fornier, F. Dal Paro, D. V. Dang, M. D’Angelo, C. J. Davies, K. Davis, R. W. Davis, A. De Antoni, S. Dear, K. Dedman, E. Defoor, M. De Haan, Th. Delaveau, S. Del Bino, M. Delgado, H. Delius, D. Delneri, F. Del Rey, J. Demolder, N. Démolis, K. Devlin, P. de Wergifosse, F. S. Dietrich, H. Ding, C. Dion, T. Dipaolo, F. Doignon, C. Doira, H. Domdey, J. Dover, Z. Du, E. Dubois, B. Dujon, M. Duncan, P. Durand, A. Düsterhöft, S. Düsterhus, T. Eki, M. El Bakkoury, L. G. Eide, K.-D. Entian, P. Eraso, D. Erdmann, H. Erfle, V. Escribano, M. Esteban, L. Fabiani, F. Fabre, C. Fairhead, B. Fartmann, A. Favello, G. Faye, H. Feldmann, L. Fernandes, F. Feroli, M. Feuermann, T. Fiedler, W. Fiers, U. N. Fleig, M. Flöth, G. M. Fobo, N. Fortin, F. Foury, M. C. Francingues-Gaillard, L. Franco, A. Fraser, J.D. Friesen, C. Fritz, L. Frontali, H. Fukuhara, L. Fulton, L. J. Fuller, C. Gabel, C. Gaillardin, L. Gaillon, F. Galibert, F. Galisson, P. Galland, F.-J. Gamo, C. Gancedo, J. M. Garcia-Cantalejo, M. I. García-Gonzalez, J. J. Garcia-Ramirez, M. García-Saéz, H. Gassenhuber, M. Gatius, S. Gattung, C. Geisel, M. E. Gent, S. Gentles, M. Ghazvini, D. Gigot, V. Gilliquet, N. Glansdorff, A. Gómez-Peris, A. Gonzaléz, S. E. Goulding, C. Granotier, T. Greco, M. Grenson, P. Grisanti, L. A. Grivell, D. Grothues, U. Gueldener, P. Guerreiro, E. Guzman, M. Haasemann, B. Habbig, H. Hagiwara, J. Hall, K. Hallsworth, N. Hamlin, N. J. Hand, V. Hanemann, J. Hani, T. Hankeln, M. Hansen, D. Harris, D. E. Harris, G. Hartzell, D. Hatat, U. Hattenhorst, J. Hawkins, U. Hebling, J. Hegemann, C. Hein, A. Hennemann, K. Hennessy, C. J. Herbert, K. Hernandez, Y. Hernando, E. Herrero, K. Heumann, D. Heuss- Neitzel, N. Hewitt, R. Hiesel, H. Hilbert, F. Hilger, L. Hillier, C. Ho, J. Hoenicka, B. Hofmann, J. Hoheisel, S. Hohmann, C. P. Hollenberg, K. Holmstrøm, O. Horaitis, T. S. Horsnell, M.-E. Huang, B. Hughes, S. Hunicke-Smith, S. Hunt, S. E. Hunt, K. Huse, R. W. Hyman, F. Iborra, K. J. Indge, I. Iraqui Houssaini, K. Isono, C. Jacq, M. Jacquet, A. Jacquier, K. Jagels, W. Jäger, C. M. James, J. C. Jauniaux, Y. Jia, M. Jier, A. Jimenez, D. Johnson, L. Johnston, M. Johnston, M. Jones, J.-L. Jonniaux, D. B. Kaback, T. Kallesøe, S. Kalman, A. Kalogeropoulos, L. Karpfinger-Hartl, D. Kashkari, C. Katsoulou, A. Kayser, A. Kelly, T. Keng, H. Keuchel, P. Kiesau, L. Kirchrath, J. Kirsten, K. Kleine, U. Kleinhans, R. Klima, C. Komp, E. Kordes, S. Korol, P. Kötter, C. Krämer, B. Kramer, P. Kreisl, T. Kucaba, H. Kuester, O. Kurdi, P. Laamanen, M. J. Lafuente, O. Landt, G. Lanfranchi, Y. Langston, D. Lashkari, P. Latreille, G. Lauquin, T. Le, P. Legrain, Y. Legros, A. Lepingle, H. Lesveque, H. Leuther, H. Lew, C. Lewis, Z. Y. Li, S. Liebl, A. Lin, D. Lin, M. Logghe, A. J. E. Lohan, E. J. Louis, G. Lucchini, K. Lutzenkirchen, R. Lyck, G. Lye, A. C. Maarse, M. J. Maat, C. Macri, A. Madania, M. Maftahi, A. Maia e Silva, E. Maillier, L. Mallet, G. Mannhaupt, V. Manus, R. Marathe, C. Marck, A. Marconi, E. Mardis, E. Martegani, R. Martin, A. Mathieu, C. T. C. Maurer, M. J. Mazón, C. Mazzoni, D. McConnell, S. McDonald, R. A. McKee, A. D. K. McReynolds, P. Melchioretto, S. Menezes, F. Messenguy, H. W. Mewes, G. Michaux, N. Miller, O. Minenkova, T. Miosga, S. Mirtipati, S. Möller-Rieker, D. Möstl, F. Molemans, A. Monnet, A-L. Monnier, M. A. Montague, M. Moro, D. Mosedale, S. Moule, L. Mouser, Y. Murakami, S. Müller-Auer, J. Mulligan, L. Murphy, M. Muzi Falconi, M. Naitou, K. Nakahara, A. Namath, F. Nasr, L. Navas, A. Nawrocki, J. Nelson, U. Nentwich, P. Netter, R. Neu, C. S. Newlon, M. Nhan, J.-M. Nicaud, R. K. Niedenthal, C. Nombela, D. Noone, R. Norgren, B. Nußbaumer, B. Obermaier, C. Odell, P. Öfner, C. Oh, K. Oliver, S. G. Oliver, B. F. Ouellette, M. Ozawa, V. Paces, C. Pallier, D. Pandolfo, L. Panzeri, S. Paoluzi, A. G. Parle-Mcdermott, S. Pascolo, N. Patricio, A. Pauley, L. Paulin, B. M. Pearson, D. Pearson, D. Peluso, J. Perea, M. Pérez-Alonso, J. E. Pérez-Ortin, A. Perrin, F. X. Petel, B. Pettersson, F. Pfeiffer, P. Philippsen, A. Piérard, E. Piravandi, R. J. Planta, P. Plevani, O. Poch, B. Poetsch, F. M. Pohl, T. M. Pohl, R. Pöhlmann, R. Poirey, D. Portetelle, F. Portillo, S. Potier, M. Proft, H. Prydz, A. Pujol, B. Purnelle, V. Puzos, M. A. Rajandream, M. Ramezani Rad, S. W. Rasmussen, A. Raynal, S. Rechmann, M. Remacha, J. L. Revuelta, P. Rice, G-F. Richard, P. Richterich, M. Rieger, L. Rifken, L. Riles, T. Rinaldi, M. Rinke, A. B. Roberts, D. Roberts, F. Rodriguez, E. Rodriguez-Belmonte, C. Rodriguez-Pousada, A. M. Rodriguez-Torres, M. Rose, R. Rossau, N. Rowley, T. Rupp, M. Ruzzi, W. Saeger, J. E. Saiz, M. Saliola, D. Salom, H. P. Saluz, M. Sánchez-Perez, M. A. Santos, E. Sanz, J. E. Sanz, A.-M. Saren, F. Sartorello, M. Sasanuma, S-I. Sasanuma, T. Scarcez, I. Schaaf-Gerstenschläger, B. Schäfer, M. Schäfer, M. Scharfe, B. Scherens, N. Schroff, M. Sen-Gupta, T. Shibata, T. Schmidheini, E. R. Schmidt, C. Schneider, P. Scholler, S. Schramm, A. Schreer, M. Schröder, C. Schwager, S. Schwarz, C. Schwarzlose, B. Schweitzer, M. Schweizer, A-M. Sdicu, P. Sehl, C. Sensen, J. G. Sgouros, T. Shogren, L. Shore, Y. Shu, J. Skala, J. Skelton, P. P. Slonimski, P. H. M. Smit, V. Smith, H. Soares, E. Soeda, A. Soler-Mira, F. Sor, N. Soriano, J. L. Souciet, C. Soustelle, R. Spiegelberg, L. I. Stateva, H. Y. Steensma, J. Stegemann, S. Steiner, L. Stellyes, F. Sterky, R. K. Storms, H. St. Peter, R. Stucka, A. Taich, E. Talla, I. Tarassov, H. Tashiro, P. Taylor, C. Teodoru, H. Tettelin, A. Thierry, G. Thireos, E. Tobiasch, D. Tovan, E. Trevaskis, Y. Tsuchiya, M. Tzermia, M. Uhlen, A. Underwood, M. Unseld, J. H. M. Urbanus, A. Urrestarazu, S. Ushinsky, M. Valens, G. Valle, A. Van Broekhoven, M. Vandenbol, Q. J. M. Van Der Aart, C. G. Van Der Linden, L. Van Dyck, M. Vanoni, J. C. Van Vliet-Reedijk, A. Vassarotti, M. Vaudin, K. Vaughan, P. Verhasselt, I. Vetter, F. Vierendeels, D. Vignati, C. Vilela, S. Vissers, C. Vleck, D. T. Vo, D. H. Vo, M. Voet, G. Volckaert, D. Von Wettstein, H. Voss, P. Vreken, G. Wagner, S. V. Walsh, R. Wambutt, H. Wang, Y. Wang, J. R. Warmington, R. Waterston, M. D. Watson, N. Weber, E. Wedler, H. Wedler, Y. Wei, S. Whitehead, B. L. Wicksteed, S. Wiemann, L. Wilcox, C. Wilson, R. Wilson, A. Winant, E. Winnett, B. Winsor, P. Wipfli, S. Wölfl, P. Wohldman, K. Wolf, K. H. Wolfe, L. F. Wright, H. Wurst, G. Xu, M. Yamasaki, M. A. Yelton, K. Yokohama, A. Yoshikawa, S. Yuping, P. Zaccaria, M. Zagulski, F. K. Zimmermann, J. Zimmermann, M. Zimmermann, W-W. Zhong, A. Zollner, and E. Zumstein

Subjects
Multidisciplinary, Computational biology, Directory, Biology, Yeast genome
Published
1997

21. Protein sequence databases: database management, data structures and data access

Author

A. Elzanowski, D. G. George, and H. W. Mewes

Subjects
Protein structure database, Information retrieval, Spatiotemporal database, Computer science, business.industry, Proteins, Data structure, Biochemistry, Database design, Data access, Text mining, Protein sequencing, Organization and Administration, Amino Acid Sequence, business, Information Systems
Published
1989

22. A standardized format for sequence data exchange

Author

D G, George, H W, Mewes, and H, Kihara

Subjects
Base Sequence, Molecular Sequence Data, Amino Acid Sequence, Information Systems
Abstract

At present there is no agreement upon a standard format for the presentation of sequence data; each of the major sequence databases has adopted their own format. As a result, efforts to pool these data and to develop software to manipulate the data have been hampered. A significant amount of software development time must be invested to handle the incompatibilities among these formats before software to solve biologically interesting problems can be implemented. In principle, the development of a standard format by the database distributors would be the best solution. However, because the databases have invested years of effort in the development of procedures specifically tailored to their own format, they are reluctant to change. Insisting that they convert to a new format would place an extreme burden on the already overtaxed resources of these groups. Furthermore, for certain specialized applications it is more efficient to present the data in nonstandard formats. An alternative solution is presented here. Rather than develop a single standard format for all sequence data, a standardized exchange format has been developed. This format was designed to serve as a common interface between the major formats currently in use. Data can be easily converted to and from it without significant loss of information. This alleviates difficulties inherent in dealing with multiple formats while preserving the local formats of the various databases.

Published
1987

23. MIPS: A database for genomes and protein sequences

Author

H W, Mewes, D, Frishman, C, Gruber, B, Geier, D, Haase, A, Kaps, K, Lemcke, G, Mannhaupt, F, Pfeiffer, C, Schüller, S, Stocker, and B, Weil

Subjects
Databases, Factual, Arabidopsis, Munich Information Center for Protein Sequences, Saccharomyces cerevisiae, Biology, computer.software_genre, Genome, Article, Set (abstract data type), Mitochondrial Proteins, Pedant, Complementary DNA, Germany, Yeasts, Databases, Genetic, Genetics, Humans, Amino Acid Sequence, Databases, Protein, Expressed Sequence Tags, Expressed sequence tag, Internet, Database, Sequence database, Base Sequence, Neurospora crassa, Genome, Human, Proteins, nucleic acids, Human genome, Genome, Fungal, computer, Genome, Plant
Abstract

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human Ep. clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz–Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91–93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155–158; Barker et al. (2001) Nucleic Acids Res., 29, 29–32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de). peerReviewed

24. The nucleotide sequence of Saccharomyces cerevisiae chromosome XV

Author

B. Dujon, K. Albermann, M. Aldea, D. Alexandraki, W. Ansorge, J. Arino, V. Benes, C. Bohn, M. Bolotin-Fukuhara, R. Bordonné, J. Boyer, A. Camasses, A. Casamayor, C. Casas, G. Chéret, C. Cziepluch, B. Daignan-Fornier, D. V. Dang, M. de Haan, H. Delius, P. Durand, C. Fairhead, H. Feldmann, L. Gaillon, F. Galisson, F.-J. Gamo, C. Gancedo, A. Goffeau, S. E. Goulding, L. A. Grivell, B. Habbig, N. J. Hand, J. Hani, U. Hattenhorst, U. Hebling, Y. Hernando, E. Herrero, K. Heumann, R. Hiesel, F. Hilger, B. Hofmann, C. P. Hollenberg, B. Hughes, J.-C. Jauniaux, A. Kalogeropoulos, C. Katsoulou, E. Kordes, M. J. Lafuente, O. Landt, E. J. Louis, A. C. Maarse, A. Madania, G. Mannhaupt, C. Marck, R. P. Martin, H. W. Mewes, G. Michaux, V. Paces, A. G. Parle-McDermott, B. M. Pearson, A. Perrin, B. Pettersson, O. Poch, T. M. Pohl, R. Poirey, D. Portetelle, A. Pujol, B. Purnelle, M. Ramezani Rad, S. Rechmann, C. Schwager, M. Schweizer, F. Sor, F. Sterky, I. A. Tarassov, C. Teodoru, H. Tettelin, A. Thierry, E. Tobiasch, M. Tzermia, M. Uhlen, M. Unseld, M. Valens, M. Vandenbol, I. Vetter, C. Vlcek, M. Voet, G. Volckaert, H. Voss, R. Wambutt, H. Wedler, S. Wiemann, B. Winsor, K. H. Wolfe, A. Zollner, E. Zumstein, and K. Kleine

Subjects
Genetics, Transposable element, Open reading frame, Multidisciplinary, biology, Centromere, Saccharomyces cerevisiae, Nucleic acid sequence, Chromosome, ORFS, biology.organism_classification, Gene
Abstract

Here we report the sequence of 569,202 base pairs of Saccharomyces cerevisiae chromosome V. Analysis of the sequence revealed a centromere, two telomeres and 271 open reading frames (ORFs) plus 13 tRNAs and four small nuclear RNAs. There are two Ty1 transposable elements, each of which contains an ORF (included in the count of 271). Of the ORFs, 78 (29%) are new, 81 (30%) have potential homologues in the public databases, and 112 (41%) are previously characterized yeast genes.

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