Dirk Metzler,
Sommersemester 2005
Mittwoch von 8:00-10:00, Seminarraum 307
Donnerstag von 14:00 bis 16:00 Uhr, Seminarraum 11
Zuordnung: ThBi, PTBi
| DNA MICROARRAYS | |||
| 18.05.2005 | Sebastian Bremm |
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| Sample size determination in microarray experiments for class comparison and prognostic classification; Biostatistics 6(1) S.27-38; Dobbin, Kevin,Simon, Richard; 2005. PDF | |||
| How many samples are needed to build a classifier: a general sequential approach; Bioinformatics 21(1) S.63-70; Carroll, Raymond J.,Dougherty, Edward R.,Fu, Wenjiang J.,Mallick, Bani; 2005. PDF | |||
| Power and sample size for DNA microarray studies; Statistics in medicine 21(23) S.3543-3570; Lee, Mei-Ling Ting,Whitmore, G. A.; 2002. PDF | |||
| RNA STRUCTURE PREDICTION | |||
| 19.05.2005 | Martina Fröhlich |
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| Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs; Journal of computational biology 10(6) S.981-995; Ieong, Samuel,Kao, Ming-Yang,Lam, Tak-Wah,Sung, Wing-Kin,Yiu, Siu-Ming; 2003. PDF | |||
| 25.05.2005 | Markus Hartenfeller |
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| The language of RNA: a formal grammar that include pseudoknots; Bioinformatics 16(4) S.334-340; Eddy, Sean R.,Rivas, Elena; 2000. PDF | |||
| Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics; BMC Bioinformatics 5(104) Giegerich, Robert,Reeder, Jens; 2004. PDF | |||
| A dynamic programming algorithm for RNA structure prediction including pseudoknots; Journal of molecular biology 285S.2053-2068; Eddy, Sean R.,Rivas, Elena; 1999. PDF | |||
| 26.05.2005 | Feiertag | ||
| 01.06.2005 | Matthias Wirth |
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| A probabilistic model for the evolution of RNA structure; BMC Bioinformatics 5(166) Holmes, Ian; 2004. PDF | |||
| RNA secondary structure prediction with simple pseudoknots; Proceedings of the second conference on asia-pacific bioinformatics 29S.239 - 246; Deogun, Jitender S.,Donis, Ruben,Komina, Olga,Ma, Fangrui; 2004. PDF | |||
| 02.06.2005 | Joanna Wisniewska |
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| Co-transcriptional folding is encoded within RNA genes; BMC Molecular Biology 5(10) Meyer, Irmtraud M.,Miklos, Istvan; 2004. PDF | |||
| Moments of boltzmann distribution for RNA secondary structures; Bulletin of Mathematical Biology Meyer, Irmtraud M.,Miklos, Istvan,Nagy, Borbala; 2005. PDF | |||
| 08.06.2005 | Natalie Jäger |
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| A graph theoretical approach to predict common RNA secondary sructure motifs including pseudoknots in unaligned sequences; Bioinformatics 20(10) S.1591-1602; Ji, Yongmei,Stormo, Gary D.,Xu, Xing; 2004. PDF | |||
| An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots; Bioinformatics 20(1) S.58-66; Ruan, Jianhua,Stormo, Gary D.,Zhang, Weixiong; 2004. PDF | |||
| Stochastic modeling of RNA pseudoknotted structures: a grammatical approach; Bioinformatics 19(1) S.i66-i73; Cai, Liming,Malmberg, Russell L.,Wu, Yunzhou; 2003. PDF | |||
| 09.06.2005 | Volker Hähnke |
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| A statistical sampling algorithm for RNA secondary structure prediction; Nucleic Acids Research 31(24) S.7280-7301; Ding, Ye,Lawrence, Charles E.; 2003. PDF | |||
| Noncoding RNA gene detection using comparative sequence analysis; BMC Bioinformatics 2(8) Eddy, Sean R.,Rivas, Elena; 2001. PDF | |||
| PHYLOGENETICS | |||
| 15.06.2005 | Fällt aus! | ||
| 16.06.2005 | Lisha Naduvilezhath |
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| Likelihood-based tests of topologies in phylogenetics; Systematic Biology 49(4) S.652-670; Anderson, Jon P.,Goldman, Nick,Rodrigo, Allen G.; 2000. PDF | |||
| 22.06.2005 | Susanne Franssen |
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| The splits in the neighbourhood of a tree; Annals of Combinatorics 8(1) S.1-11; Bryant, David; 2004. PDF | |||
| A classification of consensus methods for phylogenies; Series in Discrete Mathematics and Theoretical Computer Science 61S.163-184; Bryant, David; 2003. PDF | |||
| 23.06.2005 | Moritz Krog | ||
| A genetical theory of species selection; Journal of theoretical Biology 177(3) S.237-245; Rice, Sean H.; 1995. PDF | |||
| Directional selection and the site-frequency spectrum; Genetics 159(4) S.1779-1788; Bustamante, Carlos D.,Hartl, Daniel L.,Sawyer, Stanley,Wakeley, John; 2001. PDF | |||
| 29.06.2005 | Bianca Büttner |
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| Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution; Proceedings of the eighth annual international conference on Computational molecular biology S.326-335; Arvestad, Lars,Berglund, Ann-Charlotte,Lagergren, Jens,Sennblad, Bengt; 2004. PDF | |||
| Bayesian gene/species tree reconciliation and orthology analysis using MCMC; Bioinformatics 19(1) S.i7-i15; Arvestad, Lars,Berglund, Ann-Charlotte,Lagergren, Jens,Sennblad, Bengt; 2003. PDF | |||
| GENOMICS | |||
| 30.06.2005 | Alexander Klenner |
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| Bayesian estimation of genomic distance; Genetics 166(1) S.621-629; Durrett, Richard,Nielsen, Rasmus,York, Thomas L.; 2004. PDF | |||
| Bayesian estimation of the number of inversions in the history of two chromosomes; Journal of computational biology 9(6) S.805-818; Durrett, Richard,Nielsen, Rasmus,York, Thomas L.; 2002. PDF | |||
| Subfunctionalization: How often does it occur? How long does it take?; Theoretical Population Biology 66(2) S.93-100; Durrett, Richard,Ward, Rachel; 2004. PDF | |||
| 06.07.2005 | Ceyhun Tamer |
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| Multiple genome rearrangement; Proceedings of the second annual international conference on computational molecular biology S.243 - 247; Blanchette, Mathieu,Sankoff, David; 1998. PDF | |||
| Multiple genome rearrangement: a general approach via the evolutionary genome graph; Bioinformatics 18(1) S.303-311; Goldfarb, Lev,Korkin, Dmitry; 2002. PDF |