Algorithms for Molecular Biology, Volume 3

Volume 3, 2008

• Gang Wu, Ming-Yang Kao, Guohui Lin, Jia-Huai You:
  Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability.
  
• Malik Yousef, Segun Jung, Louise C. Showe, Michael K. Showe:
  Learning from positive examples when the negative class is undetermined- microRNA gene identification.
  
• Simon Moxon, Vincent Moulton, Jan T. Kim:
  A scoring matrix approach to detecting miRNA target sites.
  
• Gundolf Schenk, Thomas Margraf, Andrew E. Torda:
  Protein sequence and structure alignments within one framework.
  
• Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida:
  On the optimality of the neighbor-joining algorithm.
  
• Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern:
  DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.
  
• Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler:
  Noisy: Identification of problematic columns in multiple sequence alignments.
  
• Koji Kadota, Yuji Nakai, Kentaro Shimizu:
  A weighted average difference method for detecting differentially expressed genes from microarray data.
  
• Peter Meinicke, Thomas Lingner, Alexander Kaever, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Petr Karlovsky, Burkhard Morgenstern:
  Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps.
  
• Eivind Tøstesen:
  A stitch in time: Efficient computation of genomic DNA melting bubbles.
  
• Hans Binder, Knut Krohn, Stephan Preibisch:
  "Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures.
  
• Hans Binder, Stephan Preibisch:
  "Hook"-calibration of GeneChip-microarrays: Theory and algorithm.
  
• Alberto Apostolico, Olgert Denas:
  Fast algorithms for computing sequence distances by exhaustive substring composition.
  
• Christian Rödelsperger, Christoph Dieterich:
  Syntenator: Multiple gene order alignments with a gene-specific scoring function.
  
• Holger Wagner, Burkhard Morgenstern, Andreas W. M. Dress:
  Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family.
  
• Jishou Ruan, Hanzhe Chen, Lukasz A. Kurgan, Ke Chen, Chunsheng Kang, Peiyu Pu:
  HuMiTar: A sequence-based method for prediction of human microRNA targets.