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ORCIDBioinformatics, Volume 23
Volume 23, Number 1, January 2007
- Passoupathy Rajendrakumar, Akshaya Kumar Biswal
, Sena M. Balachandran, Kommoju Srinivasarao, Raman M. Sundaram:
Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. 1-4
- Waibhav Tembe, Nela Zavaljevski, Elizabeth A. Bode, Catherine Chase, Jeanne Geyer, Leonard P. Wasieloski, Gary Benson, Jaques Reifman:
Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. 5-13
- Daniel Barker, Andrew Meade, Mark Pagel:
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. 14-20
- M. Juanita Martinez, Andrew D. Smith, Bilan Li, Michael Q. Zhang, Kevin S. Harrod:
Computational prediction of novel components of lung transcriptional networks. 21-29 - Yijun Sun, Steve Goodison, Jian Li, Li Liu, William G. Farmerie:
Improved breast cancer prognosis through the combination of clinical and genetic markers. 30-37 - Hyuna Yang, Gary A. Churchill:
Estimating p-values in small microarray experiments. 38-43 - Paul Fogel, S. Stanley Young, Douglas M. Hawkins, Nathalie Ledirac:
Inferential, robust non-negative matrix factorization analysis of microarray data. 44-49 - Xiaowen Liu, Lusheng Wang:
Computing the maximum similarity bi-clusters of gene expression data. 50-56
- Jianping Hua, David W. Craig, Marcel Brun, Jennifer Webster, Victoria Zismann, Waibhav Tembe, Keta Joshipura, Matthew J. Huentelman, Edward R. Dougherty, Dietrich A. Stephan:
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. 57-63 - Johannes Dietter, Manuel Mattheisen, Robert Fürst, Franz Rüschendorf, Thomas F. Wienker, Konstantin Strauch:
Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE. 64-70 - Yujin Chung, Seung Yeoun Lee, Robert C. Elston, Taesung Park:
Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. 71-76
- Jens Hollunder, Maik Friedel, Andreas Beyer, Christopher T. Workman, Thomas Wilhelm:
DASS: efficient discovery and p-value calculation of substructures in unordered data. 77-83 - Tianhai Tian, Songlin Xu, Junbin Gao, Kevin Burrage:
Simulated maximum likelihood method for estimating kinetic rates in gene expression. 84-91 - John E. Beasley, Francisco J. Planes:
Recovering metabolic pathways via optimization. 92-98
- Ruhong Zhou, Laxmi Parida, Kush Kapila, Sudhir P. Mudur:
PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory. 99-106 - Dae-Won Kim, Ki Young Lee, Kwang H. Lee, Doheon Lee:
Towards clustering of incomplete microarray data without the use of imputation. 107-113 - Cheolhwan Oh, Stanislaw H. Zak, Hamid Mirzaei, Charles R. Buck, Fred E. Regnier, Xiang Zhang:
Neural network prediction of peptide separation in strong anion exchange chromatography. 114-118
- Guillaume Achaz, Frédéric Boyer, Eduardo P. C. Rocha, Alain Viari, Eric Coissac:
Repseek, a tool to retrieve approximate repeats from large DNA sequences. 119-121 - Gabriela G. Loots, Ivan Ovcharenko:
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. 122-124 - C. T. Kuenne, Rohit Ghai, Trinad Chakraborty, Torsten Hain:
GECO-linear visualization for comparative genomics. 125-126
- Ivica Letunic, Peer Bork:
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. 127-128
- Pak Chung Sham, Sio Iong Ao, Johnny S. H. Kwan, P. Kao, F. Cheung, Pui-Yee Fong, Michael K. Ng:
Combining functional and linkage disequilibrium information in the selection of tag SNPs. 129-131
Volume 23, Number 2, January 2007
- ECCB 2006. 1-2
- ECCB 2006 Organization. 3-4
- Sebastian Böcker:
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry. 5-12 - Yanay Ofran, Burkhard Rost:
ISIS: interaction sites identified from sequence. 13-16 - Huzefa Rangwala, George Karypis:
Incremental window-based protein sequence alignment algorithms. 17-23 - Ariel S. Schwartz, Lior Pachter:
Multiple alignment by sequence annealing. 24-29 - Dina Sokol, Gary Benson, Justin Tojeira:
Tandem repeats over the edit distance. 30-35 - Yanni Sun, Jeremy Buhler:
Designing patterns for profile HMM search. 42-43 - Abha Singh Bais, Steffen Grossmann, Martin Vingron:
Simultaneous alignment and annotation of cis-regulatory regions. 44-49 - Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, Thomas Schiex:
A comparative genome approach to marker ordering. 50-56 - Matan Gavish, Amnon Peled, Benny Chor:
Genetic code symmetry and efficient design of GC-constrained coding sequences. 57-63 - Filip Hermans, Elena Tsiporkova:
Merging microarray cell synchronization experiments through curve alignment. 64-70 - Macha Nikolski, David James Sherman:
Family relationships: should consensus reign? - consensus clustering for protein families. 71-76 - Doron Lipson, Zohar Yakhini, Yonatan Aumann:
Optimization of probe coverage for high-resolution oligonucleotide aCGH. 77-83 - Chun Ye, Eleazar Eskin:
Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. 84-90 - Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela N. Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, Roded Sharan:
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. 91-98 - Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, Hans-Peter Lenhof:
Electrostatic potentials of proteins in water: a structured continuum approach. 99-103 - 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. 104-109 - José Carlos Clemente, Kenji Satou, Gabriel Valiente:
Phylogenetic reconstruction from non-genomic data. 110-115 - Pawel Górecki, Jerzy Tiuryn:
Inferring phylogeny from whole genomes. 116-122 - Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
Efficient parsimony-based methods for phylogenetic network reconstruction. 123-128 - Matthias Bernt, Daniel Merkle, Martin Middendorf:
Using median sets for inferring phylogenetic trees. 129-135 - Matan Ninio, Eyal Privman, Tal Pupko, Nir Friedman:
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. 136-141 - Saharon Rosset:
Efficient inference on known phylogenetic trees using Poisson regression. 142-147 - Tomer Hertz, Chen Yanover:
Identifying HLA supertypes by learning distance functions. 148-155 - Keith Noto, Mark Craven:
Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects. 156-162 - Barak Raveh, Ofer Rahat, Ronen Basri, Gideon Schreiber:
Rediscovering secondary structures as network motifs - an unsupervised learning approach. 163-169 - Eitan Hirsh, Roded Sharan:
Identification of conserved protein complexes based on a model of protein network evolution. 170-176 - Natasa Przulj:
Biological network comparison using graphlet degree distribution. 177-183 - Oleg Rokhlenko, Ydo Wexler, Zohar Yakhini:
Similarities and differences of gene expression in yeast stress conditions. 184-190 - Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm:
TOPP - the OpenMS proteomics pipeline. 191-197 - Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, Andrew Emili:
Difference detection in LC-MS data for protein biomarker discovery. 198-204 - Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer:
Vorolign - fast structural alignment using Voronoi contacts. 205-211 - Angela Enosh, Sarel Jacob Fleishman, Nir Ben-Tal, Dan Halperin:
Prediction and simulation of motion in pairs of transmembrane alpha-helices. 212-218 - Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik:
Using an alignment of fragment strings for comparing protein structures. 219-224 - Etai Jacob, Ron Unger:
A tale of two tails: why are terminal residues of proteins exposed? 225-230 - 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. 231-236 - Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, Peter Stoehr:
EBIMed - text crunching to gather facts for proteins from Medline. 237-244
- Alfonso Valencia, Alex Bateman:
Editorial. 133
- Helge G. Roider, Aditi Kanhere, Thomas Manke, Martin Vingron:
Predicting transcription factor affinities to DNA from a biophysical model. 134-141 - Snorre A. Helvik, Ola R. Snøve Jr., Pål Sætrom:
Reliable prediction of Drosha processing sites improves microRNA gene prediction. 142-149
- 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. 150-155 - Michael Farrar:
Striped Smith-Waterman speeds database searches six times over other SIMD implementations. 156-161 - Xu Zhang, Tamer Kahveci:
QOMA: quasi-optimal multiple alignment of protein sequences. 162-168
- Zhu Yang, John D. O'Brien, Xiaobin Zheng, Huaiqiu Zhu, Zhen-Su She:
Tree and rate estimation by local evaluation of heterochronous nucleotide data. 169-176
- Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan:
In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. 177-183
- Jorn R. de Haan, Ron Wehrens, Susanne Bauerschmidt, Ester Piek, René C. van Schaik, Lutgarde M. C. Buydens:
Interpretation of ANOVA models for microarray data using PCA. 184-190 - Andreas W. Schreiber, Ute Baumann:
A framework for gene expression analysis. 191-197
- Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zhang-Zhi Hu, Cathy H. Wu:
Dependence network modeling for biomarker identification. 198-206 - Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann:
Modular organization of protein interaction networks. 207-214 - Xiaotu Ma, Hyunju Lee, Li Wang, Fengzhu Sun:
CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. 215-221 - Ai Li, Steve Horvath:
Network neighborhood analysis with the multi-node topological overlap measure. 222-231
- Yuanyuan Tian, Richard C. McEachin, Carlos Santos, David J. States, Jignesh M. Patel:
SAGA: a subgraph matching tool for biological graphs. 232-239
- 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. 240-242 - Nicolás Bellora, Domènec Farré, M. Mar Albà:
PEAKS: identification of regulatory motifs by their position in DNA sequences. 243-244
- Sinae Kim, Jerry W. Tsai, Ioannis Kagiampakis, Patricia LiWang, Marina Vannucci:
Detecting protein dissimilarities in multiple alignments using Bayesian variable selection. 245-246
- R. Cathelin, F. Lopez, Christophe Klopp:
AGScan: a pluggable microarray image quantification software based on the ImageJ library. 247-248
- 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. 249-251 - K. Hao, Xiaojun Di, Simon Cawley:
LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage. 252-254 - Shaun Purcell, Mark J. Daly, Pak Chung Sham:
WHAP: haplotype-based association analysis. 255-256
- Seth Falcon, Robert Gentleman:
Using GOstats to test gene lists for GO term association. 257-258
- Christopher S. Poultney, Rodrigo A. Gutiérrez, Manpreet S. Katari, Miriam L. Gifford, W. Bradford Paley, Gloria M. Coruzzi, Dennis E. Shasha:
Sungear: interactive visualization and functional analysis of genomic datasets. 259-261 - J. A. Falkner, J. W. Falkner, P. C. Andrews:
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats. 262-263 - 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. 264-265
- CASPAR: a hierarchical Bayesian approach to predict survival times in cancer from gene expression data. 266
Volume 23, Number 3, 1 February 2007
- Richard Thilakaraj, Krishnan Raghunathan, Sharmila Anishetty, Pennathur Gautam:
In silico identification of putative metal binding motifs. 267-271
- Alexander P. Gultyaev, Hans A. Heus, René C. L. Olsthoorn:
An RNA conformational shift in recent H5N1 influenza A viruses. 272-276
- Roger Higdon, Eugene Kolker:
A predictive model for identifying proteins by a single peptide match. 277-280
- Liang Goh, Susan K. Murphy, Sayan Mukherjee, Terrence S. Furey:
Genomic sweeping for hypermethylated genes. 281-288
- Jaebum Kim, Saurabh Sinha:
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. 289-297
- Ian B. Jeffery, Stephen F. Madden, Paul A. McGettigan, Guy Perrière, Aedín C. Culhane, Desmond G. Higgins:
Integrating transcription factor binding site information with gene expression datasets. 298-305 - Zhen Jiang, Robert Gentleman:
Extensions to gene set enrichment. 306-313 - Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D. Dynlacht, Guangliang Chen, Bud Mishra:
Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data. 314-320 - Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H. Scheuermann:
A distribution free summarization method for Affymetrix GeneChip® arrays. 321-327 - Kenneth Lo, Raphael Gottardo:
Flexible empirical Bayes models for differential gene expression. 328-335
- L. Jason Steggles, Richard Banks, Oliver Shaw, Anil Wipat:
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. 336-343 - Christian Klukas, Falk Schreiber:
Dynamic exploration and editing of KEGG pathway diagrams. 344-350 - Andrea L. Knorr, Rishi Jain, Ranjan Srivastava:
Bayesian-based selection of metabolic objective functions. 351-357 - Neda Bagheri, Jörg Stelling, Francis J. Doyle III:
Quantitative performance metrics for robustness in circadian rhythms. 358-364
- Katrin Fundel, Robert Küffner, Ralf Zimmer:
RelEx - Relation extraction using dependency parse trees. 365-371
- Kazutaka Katoh, Hiroyuki Toh:
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. 372-374
- Kreshna Gopal, Erik McKee, Tod D. Romo, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger:
Crystallographic protein model-building on the web. 375-377 - Lisa Fukui, Yuan Chen:
NvMap: automated analysis of NMR chemical shift perturbation data. 378-380 - Wolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Therese E. Malliavin, Michael Nilges:
ARIA2: Automated NOE assignment and data integration in NMR structure calculation. 381-382 - Stephen A. Cammer:
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol. 383-384 - Emidio Capriotti, Rita Casadio:
K-Fold: a tool for the prediction of the protein folding kinetic order and rate. 385-386
- Giorgio Valentini:
Mosclust: a software library for discovering significant structures in bio-molecular data. 387-389 - Ignacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo:
Prophet, a web-based tool for class prediction using microarray data. 390-391
- Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss, Richard Bonneau:
BioNetBuilder: automatic integration of biological networks. 392-393