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Bioinformatics Journal
SIGSIM: Systems Biology of E.coli

Accepted Papers - Presentation Order
(Abstracts will be posted as they become available)

PAPERS 1: Phylogeny and Genome Rearrangements

1. Detection and validation of single gene inversions. Jean-Francois Lefebvre,Nadia El-Mabrouk, Elizabeth Tillier and David Sankoff [Download Abstract as a PDF]

2. Fast identification and Statistical Evaluation of Segmental Homologies in Comparative Maps. Peter P. Calabrese, Sugata Chakravarty and Todd J. Vision [Download Abstract as a PDF]

3. Glocal Alignment: Finding Rearrangements During Alignment. Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou [Download Abstract as a PDF]

4. Bayesian Gene/Species Tree Reconciliation and Orthology Analysis Using MCMC. Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren and Bengt Sennblad [Download Abstract as a PDF]

5. Scaling Up Accurate Phylogenetic Reconstruction from Gene-Order Data. Jijun Tang and Bernard Moret [Download Abstract as a PDF]

6. Deriving phylogenetic trees from the similarity analysis of metabolic pathways. Maureen Heymans and Ambuj Singh [Download Abstract as a PDF]

PAPERS 2: Expression Arrays and Networks

7. Using Hidden Markov Models to Analyze Gene Expression Time Course Data. Alexander Schliep, Alexander Schonhuth, and Christine Steinhoff [Download Abstract as a PDF]

8. Combining Multiple Microarray Studies and Modeling Interstudy Variation. Jung Kyoon Choi, Ung Sik Yu, Sangsoo Kim, and Ook Joon Yoo [Download Abstract as a PDF]

9. Gene Structure-Based Splice Variant Deconvolution Using a Microarray Platform. Hui Wang, Earl Hubbell, Jing-shan Hu, Gangwu Mei, Melissa Cline, and Gang Lu [Download Abstract as a PDF]

10. Discovering Molecular Pathways from Protein Interaction and Gene Expression Data. Eran Segal, Haidong Wang, and Daphe Koller [Download Abstract as a PDF]

11. Chain Functions and Scoring Functions in Genetic Networks. Ron Shamir and Irit Gat Viks [Download Abstract as a PDF]

PAPERS 3: Predicting Clinical Outcomes

12. Predicting Phenotype from Patterns of Annotation. Oliver King, Jeff Lee, Aimee Dudley, Daniel Janse, George Church, and Frederick Roth [Download Abstract as a PDF]

13. Methods for Optimizing Antiviral Combination Therapies. Niko Beerenwinkel, Thomas Lengauer, Martin Daumer, Rolf Kaiser, Hauke Walter,Klaus Korn, Daniel Hoffman and Joachim Selbig [Download Abstract as a PDF]


1. Widespread Nonsense-mediated mRNA Decay of Normal and Disease Genes. Richard E. Green, Benjamin P. Lewis, R. Tyler Hillman, Marcho Blanchette, Liana F. Lareau, Aaron T. Garnett, Donald C. Rio, and Steven E. Brenner [Download Abstract as a PDF]

2. Skew in CG Content Near the Transcription Start Site in Arabidopsis thaliana. Tatiana Tatarinova, Vyacheslav Brover, Maxim Troukhan, and Nickolai Alexandrov [Download Abstract as a PDF]

3. A New Approach to the Annotation of Bacterial Genomes using Phylogenomic Profiles. F. Enault, K. Suhre, C. Abergel, O. Poirot, and J-M Claverie [Download Abstract as a PDF]

4. GeneLoc: Exon-based Integration of Human Genome Maps. Naomi Rosen, Vered Chalifa-Caspi, Orit Shmueli, Avital Adato, Michal Lapidot, Julie Stampnitzky, Marilyn Safran, and Doron Lancet [Download Abstract as a PDF]

5. Linking Genotype to Phenotype: The International Rice Information System (IRIS). Richard Bruskiewich, Alexander Cosico, William Eusebio,Arllet Portugal, Luralyn Ramos, Graham McLaren [Download Abstract as a PDF]

6. Talisman - Rapid Application Development for the Grid. Tom Oinn [Download Abstract as a PDF]

7. myGrid: Personalised Bioinformatics on the Information Grid. Stevens Robert, Alan Robinson, and Carole Goble [Download Abstract as a PDF]


8. GENIA Corpus - A Semantically Annotated Corpus for Bio-textmining. Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, and Jun'ichi Tsujii [Download Abstract as a PDF]

9. Combining NLP and Probabilistic Categorisation for Document and Term Selectionfor SWISS-PROT Medical Annotation. Pavel B. Dobrokhotov, Cyril Goutte, Anne-Lise Veuthey, and Eric Gaussier [Download Abstract as a PDF]

10. Complexity Management in Visualizing Protein Interaction Networks. Byong-Hyon Ju and Kyungsook Han [Download Abstract as a PDF]

11. PSI: Indexing Protein Structures for Fast Similarity Search. Orhan Camoglu, Tamer Kahveci, and Ambuj Singh [Download Abstract as a PDF]

12. WIthdrawn

13. A Tool to Assist the Sudy of Specific Features at Protein Binding Sites. Francisco Melo [Download Abstract as a PDF]

PAPERS 4: Protein Clustering, Alignment, and Patterns

14. APDB:A Novel Measure for Benchmarking Sequence Alignment Methods without Reference Alignments.
Orla Osullivan, Marc Zehnder, Des Higgins, Philipp Bucher, Aurelien Grosdidier, and Notredame Cedric [Download Abstract as a PDF]

15. Remote Homology Detection: A Motif Based Approach. Asa Ben-Hur and Douglas Brutlag [Download Abstract as a PDF]

16. Detecting Protein Sequence Conservation via Metric Embeddings. Eran Halperin, Jeremy Buhler, Richard Karp, Robert Krauthgamer, and Ben Westover [Download Abstract as a PDF]

17. Sensitive Pattern Discovery with 'Fuzzy' Alignments of Distantly Related Proteins. Andreas Heger and Liisa Holm [Download Abstract as a PDF]

18. Extraction of Correlated Gene Clusters from Multiple Genomic Data by Generalized Kernel Canonical Correlation Analysis.
Yoshihiro Yamanishi, Jean-Philippe Vert, Akihiro Nakaya, and Minoru Kanehisa [Download Abstract as a PDF]

19. A Probabilistic Approach to Gene Function Assignment and Propagation in Protein Interaction Networks. Stanley Letovsky and Simon Kasif [Download Abstract as a PDF]

PAPERS 5: Transcription Motifs and Modules

20. Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. Ojvind Johansson, Wyeth W. Wasserman, and Jens Lagergren [Download Abstract as a PDF]

21. CREME: A Framework for Identifying Cis-Regulatory Modules in Human-Mouse Conserved Segments. Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, and Richard Karp [Download Abstract as a PDF]

22. A Probabilistic Method to Detect Regulatory Modules. Saurabh Sinha, Erik van Nimwegen, and Eric Siggia [Download Abstract as a PDF]

23. Predicting Bacterial Transcription Units using Sequence and Expression Data. Joseph Bockhorst, Yu Qiu, Jeremy Glasner, Mingzhu Liu, Frederick Blattner,and Mark Craven [Download Abstract as a PDF]

24. Genome-wide Discovery of Transcriptional Modules from DNA Sequence and Gene Expression. Eran Segal, Roman Yelensky, and Daphne Koller [Download Abstract as a PDF]

PAPERS 6: Structure and HMMs

25. Stochastic Modeling of RNA Pseudoknotted Structures: A Grammatical Approach. Liming Cai, Russell Malmberg, and Yunzhou Wu [Download Abstract as a PDF]

26. Pair Hidden Markov Models on Tree Structures. Yasubumi Sakakibara [Download Abstract as a PDF]

27. Using Guide Trees to Construct Multiple-Sequence Evolutionary HMMs. Ian Holmes [Download Abstract as a PDF]

28. MASS: A Method for Multiple Structural Alignment by Secondary Structures. Oranit Dror, Hadar Benyamini, Ruth Nussinov, and Haim Wolfson [Download Abstract as a PDF]

29. Protein Structure Prediction via Combinatorial Assembly of Sub-structural Units. Yuval Inbar, Hadar Benyamini, Ruth Nussinov, and Haim Wolfson [Download Abstract as a PDF]

30. An ENSEMBLE Machine Learning Approach for the Prediction of All-Alpha Membrane Proteins. Pier Luigi Martelli, Piero Fariselli, and Rita Casadio [Download Abstract as a PDF]

PAPERS 7: Text Mining and High Throughput Methods

31. The Discovery Net System for High Throughput Bioinformatics. Anthony Rowe, Yike Guo, Dimitrios Kalaitzopoulos, Michelle Osmond, and Moustafa Ghanem [Download Abstract as a PDF]

32. Processing of the Natural Language Queries to a Relational Database. Maria Samsonova, Andrei Pisarev, and Maxim Blagov [Download Abstract as a PDF]

33. Evaluation of Text Data Mining for Database Curation: Lessons Learned from the KDD Challenge Cup. Alexander Yeh, Lynette Hirschman, and Alexander Morgan [Download Abstract as a PDF]

34. Extracting Synonymous Gene and Protein Terms from Biological Literature. Hong Yu and Eugene Agichtein [Download Abstract as a PDF]

35. SNP and Mutation Discovery using Base-Specific Cleavage and MALDI-TOF Mass Spectrometry. Sebastian Boecker [Download Abstract as a PDF]