Volume 34, Number 1, February 2010

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  William R. Taylor, Zoe Katsimitsoulia: A soft collision detection algorithm for simple Brownian dynamics. 1-10
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  Jeyaraman Srividhya, Márcio A. Mourão, Edmund J. Crampin, Santiago Schnell: Enzyme catalyzed reactions: From experiment to computational mechanism reconstruction. 11-18
• 
  Srboljub M. Mijailovich, Xiaochuan Li, Juan C. del Álamo, R. Hugh Griffiths, Vojislav Kecman, Michael A. Geeves: Resolution and uniqueness of estimated parameters of a model of thin filament regulation in solution. 19-33
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  Kateryna Mishchenko, Lars Rönnegård, Sverker Holmgren, Volodymyr Mishchenko: Assessing a multiple QTL search using the variance component model. 34-41
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  Alexander Zawaira, Marco Gallotta, Natasha Beeton-Kempen, Lauren Coulson, Patrick Marais, Michelle Kuttel, Jonathan Blackburn: Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450 (CYP) and P450-oxidoreductase (POR) proteins. 42-52
• 
  Takuyo Aita, Koichi Nishigaki, Yuzuru Husimi: Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential. 53-62

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  DongMing Tang, Qingxin Zhu, Fan Yang: A Poisson-based adaptive affinity propagation clustering for SAGE data. 63-70

Volume 34, Number 2, April 2010

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  Zoe Katsimitsoulia, William R. Taylor: A hierarchic collision detection algorithm for simple Brownian dynamics. 71-79
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  Hervé Seligmann: The ambush hypothesis at the whole-organism level: Off frame, 'hidden' stops in vertebrate mitochondrial genes increase developmental stability. 80-85
• 
  Elsje Pienaar, Aaron M. Fluitt, Scott E. Whitney, Alison G. Freifeld, Hendrik J. Viljoen: A model of tuberculosis transmission and intervention strategies in an urban residential area. 86-96
• 
  Jacob D. Durrant, James Andrew McCammon: Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. 97-105
• 
  Jun Hu, Huimin Li, Jing Zhang: Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast. 106-114

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  Piotr Waligórski, Maciej Szaleniec: Prediction of white cabbage (Brassica oleracea var. capitata) self-incompatibility based on neural network and discriminant analysis of complex electrophoretic patterns. 115-121
• 
  Christian J. Michel, Giuseppe Pirillo: Identification of all trinucleotide circular codes. 122-125
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  R. Sabarinathan, Raunak Basu, Krishna Sekar: ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. 126-130
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  In-Seon Jeong, Kyoung-Wook Park, Seung-Ho Kang, Hyeong-Seok Lim: An efficient similarity search based on indexing in large DNA databases. 131-136

Volume 34, Number 3, June 2010

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  Chenhua Huang, Xiangbo Yang, Zhihong He: Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures. 137-142
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  Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja: Dynamical effects of transcriptional pause-prone sites. 143-148
• 
  Kang Ning: Deposition and extension approach to find longest common subsequence for thousands of long sequences. 149-157
• 
  Christian Meesters, Bruno Pairet, Anja Rabenhorst, Heinz Decker, Elmar Jaenicke: Monte Carlo-based rigid body modelling of large protein complexes against small angle scattering data. 158-164
• 
  Li Guo, Zuhong Lu: Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. 165-171
• 
  Hyun Joo, Xiaotao Qu, Rosemarie Swanson, C. Michael McCallum, Jerry W. Tsai: Fine grained sampling of residue characteristics using molecular dynamics simulation. 172-183
• 
  Francisco Javier Burguillo Muñoz, Javier Martin, Inmaculada Barrera, William G. Bardsley: Meta-analysis of microarray data: The case of imatinib resistance in chronic myelogenous leukemia. 184-192
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  Sebastian Schneckener, Linus Görlitz, Heidrun Ellinger-Ziegelbauer, Hans-Jürgen Ahr, Andreas Schuppert: An elastic network model to identify characteristic stress response genes. 193-202
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  Olfa Siala, Ahmed Rebai, Faouzi Baklouti, Faiza Fakhfakh: Subtle discrepancies of SF2/ASF ESE sequence motif among human tissues: A computational approach. 203-209

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  Nalin C. W. Goonesekere, Krysten Shipely, Kevin O'Connor: The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. 210-214

Volume 34, Number 4, August 2010

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  Zengyou He, Weichuan Yu: Stable feature selection for biomarker discovery. 215-225

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  Bashistha Kumar Kanth, Kwangkyoung Liou, Jae Kyung Sohng: Homology modeling, binding site identification and docking in flavone hydroxylase CYP105P2 in Streptomyces peucetius ATCC 27952. 226-231
• 
  Sheng Lin, William K. C. Cheung, Shen Chen, Gang Lu, Zifeng Wang, Dan Xie, Kui Li, Marie C. M. Lin, Hsiang-fu Kung: Computational identification and characterization of primate-specific microRNAs in human genome. 232-241

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  Irina V. Zorkoltseva, Yurii S. Aulchenko, Cornelia M. van Duijn, Tatiana I. Axenovich: Ped_Outlier software for automatic identification of within-family outliers. 242-243
• 
  Emmanuel Martinez, Mario Moises Alvarez, Victor Trevino: Compact cancer biomarkers discovery using a swarm intelligence feature selection algorithm. 244-250
• 
  Yanming Zou, Chun Hou: Systematic analysis of an amidase domain CHAP in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. 251-257

Volume 34, Numbers 5-6, December 2010

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  Sophie Lèbre, Christian J. Michel: A stochastic evolution model for residue Insertion-Deletion Independent from Substitution. 259-267
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  Omodele Ibraheem, Christiaan E. J. Botha, Graeme Bradley: In silico analysis of cis-acting regulatory elements in 5' regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. 268-283
• 
  Sudhakar Sahoo, Andreas Alexander Albrecht: Ranking of microRNA target prediction scores by Pareto front analysis. 284-292

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  Efendi N. Nasibov, Sezin Tunaboylu: Classification of splice-junction sequences via weighted position specific scoring approach. 293-299
• 
  Piotr Plonski, Jan P. Radomski: Quick path finding - Quick algorithmic solution for unambiguous labeling of phylogenetic tree nodes. 300-307
• 
  Ming Chen, Yijun Meng, Haibin Gu, Dijun Chen: Functional characterization of plant small RNAs based on next-generation sequencing data. 308-312
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  Ping Gong, Fuliang Xie, Baohong Zhang, Edward J. Perkins: In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. 313-319
• 
  Sitanshu Sekhar Sahu, Ganapati Panda: A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. 320-327
• 
  Daniel Reker, Stefan Katzenbeisser, Kay Hamacher: Computation of mutual information from Hidden Markov Models. 328-333

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