| 5 | -- | 12 | Sebastian Böcker. Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry |
| 13 | -- | 16 | Yanay Ofran, Burkhard Rost. ISIS: interaction sites identified from sequence |
| 17 | -- | 23 | Huzefa Rangwala, George Karypis. Incremental window-based protein sequence alignment algorithms |
| 24 | -- | 29 | Ariel S. Schwartz, Lior Pachter. Multiple alignment by sequence annealing |
| 30 | -- | 35 | Dina Sokol, Gary Benson, Justin Tojeira. Tandem repeats over the edit distance |
| 42 | -- | 43 | Yanni Sun, Jeremy Buhler. Designing patterns for profile HMM search |
| 44 | -- | 49 | Abha Singh Bais, Steffen Grossmann, Martin Vingron. Simultaneous alignment and annotation of ::::cis::::-regulatory regions |
| 50 | -- | 56 | Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, Thomas Schiex. A comparative genome approach to marker ordering |
| 57 | -- | 63 | Matan Gavish, Amnon Peled, Benny Chor. Genetic code symmetry and efficient design of GC-constrained coding sequences |
| 64 | -- | 70 | Filip Hermans, Elena Tsiporkova. Merging microarray cell synchronization experiments through curve alignment |
| 71 | -- | 76 | Macha Nikolski, David James Sherman. Family relationships: should consensus reign? - consensus clustering for protein families |
| 77 | -- | 83 | Doron Lipson, Zohar Yakhini, Yonatan Aumann. Optimization of probe coverage for high-resolution oligonucleotide aCGH |
| 84 | -- | 90 | Chun Ye, Eleazar Eskin. Discovering tightly regulated and differentially expressed gene sets in whole genome expression data |
| 91 | -- | 98 | Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, Roded Sharan. A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data |
| 99 | -- | 103 | Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, Hans-Peter Lenhof. Electrostatic potentials of proteins in water: a structured continuum approach |
| 104 | -- | 109 | Rafael Najmanovich, Abdellah Allali-Hassani, Richard J. Morris, Ludmila Dombrovsky, Patricia W. Pan, Masoud Vedadi, Alexander N. Plotnikov, Aled M. Edwards, Cheryl H. Arrowsmith, Janet M. Thornton. Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family |
| 110 | -- | 115 | José Carlos Clemente, Kenji Satou, Gabriel Valiente. Phylogenetic reconstruction from non-genomic data |
| 116 | -- | 122 | Pawel Górecki, Jerzy Tiuryn. Inferring phylogeny from whole genomes |
| 123 | -- | 128 | Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller. Efficient parsimony-based methods for phylogenetic network reconstruction |
| 129 | -- | 135 | Matthias Bernt, Daniel Merkle, Martin Middendorf. Using median sets for inferring phylogenetic trees |
| 133 | -- | 0 | Alfonso Valencia, Alex Bateman. Editorial |
| 134 | -- | 141 | Helge G. Roider, Aditi Kanhere, Thomas Manke, Martin Vingron. Predicting transcription factor affinities to DNA from a biophysical model |
| 136 | -- | 141 | Matan Ninio, Eyal Privman, Tal Pupko, Nir Friedman. Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates |
| 142 | -- | 147 | Saharon Rosset. Efficient inference on known phylogenetic trees using Poisson regression |
| 142 | -- | 149 | Snorre A. Helvik, Ola R. Snøve Jr., Pål Sætrom. Reliable prediction of Drosha processing sites improves microRNA gene prediction |
| 148 | -- | 155 | Tomer Hertz, Chen Yanover. Identifying HLA supertypes by learning distance functions |
| 150 | -- | 155 | Richard J. Dixon, Ian C. Eperon, Nilesh J. Samani. Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression |
| 156 | -- | 161 | Michael Farrar. Striped Smith-Waterman speeds database searches six times over other SIMD implementations |
| 156 | -- | 162 | Keith Noto, Mark Craven. Learning probabilistic models of ::::cis::::-regulatory modules that represent logical and spatial aspects |
| 162 | -- | 168 | Xu Zhang, Tamer Kahveci. QOMA: quasi-optimal multiple alignment of protein sequences |
| 163 | -- | 169 | Barak Raveh, Ofer Rahat, Ronen Basri, Gideon Schreiber. Rediscovering secondary structures as network motifs - an unsupervised learning approach |
| 169 | -- | 176 | Zhu Yang, John D. O Brien, Xiaobin Zheng, Huaiqiu Zhu, Zhen-Su She. Tree and rate estimation by local evaluation of heterochronous nucleotide data |
| 170 | -- | 176 | Eitan Hirsh, Roded Sharan. Identification of conserved protein complexes based on a model of protein network evolution |
| 177 | -- | 183 | Natasa Przulj. Biological network comparison using graphlet degree distribution |
| 177 | -- | 183 | Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan. ::::In silico:::: grouping of peptide/HLA class I complexes using structural interaction characteristics |
| 184 | -- | 190 | Oleg Rokhlenko, Ydo Wexler, Zohar Yakhini. Similarities and differences of gene expression in yeast stress conditions |
| 184 | -- | 190 | J. R. de Haan, Ron Wehrens, S. Bauerschmidt, E. Piek, René C. van Schaik, Lutgarde M. C. Buydens. Interpretation of ANOVA models for microarray data using PCA |
| 191 | -- | 197 | Andreas W. Schreiber, Ute Baumann. A framework for gene expression analysis |
| 191 | -- | 197 | Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm. TOPP - the OpenMS proteomics pipeline |
| 198 | -- | 204 | Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, Andrew Emili. Difference detection in LC-MS data for protein biomarker discovery |
| 198 | -- | 206 | Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zhang-Zhi Hu, Cathy H. Wu. Dependence network modeling for biomarker identification |
| 205 | -- | 211 | Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer. Vorolign - fast structural alignment using Voronoi contacts |
| 207 | -- | 214 | Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger Chang, Jizhong Zhou, Richard H. Scheuermann. Modular organization of protein interaction networks |
| 212 | -- | 218 | Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, Dan Halperin. Prediction and simulation of motion in pairs of transmembrane alpha-helices |
| 215 | -- | 221 | Xiaotu Ma, Hyunju Lee, Li Wang, Fengzhu Sun. CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data |
| 219 | -- | 224 | Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik. Using an alignment of fragment strings for comparing protein structures |
| 222 | -- | 231 | Ai Li, Steve Horvath. Network neighborhood analysis with the multi-node topological overlap measure |
| 225 | -- | 230 | Etai Jacob, Ron Unger. A tale of two tails: why are terminal residues of proteins exposed? |
| 231 | -- | 236 | Annalisa Marsico, Dirk Labudde, K. Tanuj Sapra, Daniel J. Muller, Michael Schroeder. A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy |
| 232 | -- | 239 | Yuanyuan Tian, Richard C. McEachin, Carlos Santos, David J. States, Jignesh M. Patel. SAGA: a subgraph matching tool for biological graphs |
| 237 | -- | 244 | Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, Peter Stoehr. EBIMed - text crunching to gather facts for proteins from Medline |
| 240 | -- | 242 | Frank M. You, Ming-Cheng Luo, Yong Qiang Gu, Gerard R. Lazo, Karin Deal, Jan Dvorak, Olin D. Anderson. GenoProfiler: batch processing of high-throughput capillary fingerprinting data |
| 243 | -- | 244 | Nicolás Bellora, Domènec Farré, M. Mar Albà. PEAKS: identification of regulatory motifs by their position in DNA sequences |
| 245 | -- | 246 | Sinae Kim, Jerry Tsai, Ioannis Kagiampakis, Patricia LiWang, Marina Vannucci. Detecting protein dissimilarities in multiple alignments using Bayesian variable selection |
| 247 | -- | 248 | R. Cathelin, F. Lopez, Ch. Klopp. AGScan: a pluggable microarray image quantification software based on the ImageJ library |
| 249 | -- | 251 | Reagan J. Kelly, Douglas M. Jacobsen, Yan V. Sun, Jennifer A. Smith, Sharon L. R. Kardia. KGraph: a system for visualizing and evaluating complex genetic associations |
| 252 | -- | 254 | K. Hao, X. Di, S. Cawley. LdCompare: rapid computation of single- and multiple-marker ::::r:::::::2::: and genetic coverage |
| 255 | -- | 256 | Shaun Purcell, Mark J. Daly, Pak Chung Sham. WHAP: haplotype-based association analysis |
| 257 | -- | 258 | Seth Falcon, Robert Gentleman. Using GOstats to test gene lists for GO term association |
| 259 | -- | 261 | Christopher S. Poultney, Rodrigo A. Gutiérrez, Manpreet S. Katari, Miriam L. Gifford, W. Bradford Paley, Gloria M. Coruzzi, Dennis Shasha. Sungear: interactive visualization and functional analysis of genomic datasets |
| 262 | -- | 263 | J. A. Falkner, J. W. Falkner, P. C. Andrews. ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats |
| 264 | -- | 265 | Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida. PrepMS: TOF MS data graphical preprocessing tool |