Volume 6,
2005
- Aditi Kanhere, Manju Bansal:
A novel method for prokaryotic promoter prediction based on DNA stability.
1
- David A. Rasko, Garry S. A. Myers, Jacques Ravel:
Visualization of comparative genomic analyses by BLAST score ratio.
2
- Les Dethlefsen, Thomas M. Schmidt:
Differences in codon bias cannot explain differences in translational power among microbes.
3
- Jean-Christophe Gelly, Laurent Chiche, Jérôme Gracy:
EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.
4
- Marko Srdanovic, Ulf Schenk, Michael Schwieger, Fabien Campagne:
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases.
5
- Dave Bridges, Marie E. Fraser, Greg B. G. Moorhead:
Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes.
6
- Pantelis G. Bagos, Theodore Liakopoulos, Stavros J. Hamodrakas:
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.
7
- Dongxiao Zhu, Zhaohui S. Qin:
Structural comparison of metabolic networks in selected single cell organisms.
8
- David A. Nix, Michael B. Eisen:
GATA: a graphic alignment tool for comparative sequence analysis.
9
- Helene H. Thygesen, Aeilko H. Zwinderman:
Modelling the correlation between the activities of adjacent genes in drosophila.
10
- Thomas MacCarthy, Andrew Pomiankowski, Robert Seymour:
Using large-scale perturbations in gene network reconstruction.
11
- Ran Rubinstein, Itamar Simon:
MILANO - custom annotation of microarray results using automatic literature searches.
12
- Francisco Azuaje, Haiying Wang, Alban Chesneau:
Non-linear mapping for exploratory data analysis in functional genomics.
13
- Deli Wang, Jian Huang, Hehuang Xie, Liliana Manzella, Marcelo Bento Soares:
A robust two-way semi-linear model for normalization of cDNA microarray data.
14
- Antje Krause, Jens Stoye, Martin Vingron:
Large scale hierarchical clustering of protein sequences.
15
- William H. Majoros, Mihaela Pertea, Arthur L. Delcher, Steven Salzberg:
Efficient decoding algorithms for generalized hidden Markov model gene finders.
16
- Don Simone Daly, Amanda M. White, Susan M. Varnum, Kevin K. Anderson, Richard C. Zangar:
Evaluating concentration estimation errors in ELISA microarray experiments.
17
- Rifat A. Hamoudi, Amina El-Hamidi, Ming-Qing Du:
Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software).
18
- Vilmos Ágoston, Masa Cemazar, László Kaján, Sándor Pongor:
Graph-representation of oxidative folding pathways.
19
- Pengyu Hong, Wing Hung Wong:
GeneNotes - A novel information management software for biologists.
20
- John L. Moreland, Apostol Gramada, Oleksandr V. Buzko, Qing Zhang, Philip E. Bourne:
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.
21
- Maria Novatchkova, Andreas Bachmair, Birgit Eisenhaber, Frank Eisenhaber:
Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family.
22
- Joe Whitney, David J. Esteban, Chris Upton:
Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches.
23
- Victor Kunin, Christos A. Ouzounis:
Clustering the annotation space of proteins.
24
- Sylvain Foissac, Thomas Schiex:
Integrating alternative splicing detection into gene prediction.
25
- Kerby Shedden, Wei Chen, Rork Kuick, Debashis Ghosh, James W. MacDonald, Kathleen R. Cho, Thomas J. Giordano, Stephen B. Gruber, Eric R. Fearon, Jeremy M. G. Taylor, Samir Hanash:
Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.
26
- Franck Picard, Stéphane Robin, Marc Lavielle, Christian Vaisse, Jean-Jacques Daudin:
A statistical approach for array CGH data analysis.
27
- Yingdong Zhao, Ming-Chung Li, Richard Simon:
An adaptive method for cDNA microarray normalization.
28
- Harold J. Drabkin, Christopher Hollenbeck, David P. Hill, Judith A. Blake:
Ontological visualization of protein-protein interactions.
29
- Alena Shmygelska, Holger H. Hoos:
An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem.
30
- Guy St. C. Slater, Ewan Birney:
Automated generation of heuristics for biological sequence comparison.
31
- James A. Koziol, Anne C. Feng:
A note on generalized Genome Scan Meta-Analysis statistics.
32
- Shandar Ahmad, Akinori Sarai:
PSSM-based prediction of DNA binding sites in proteins.
33
- Sohrab P. Shah, Yong Huang, Tao Xu, Macaire M. S. Yuen, John Ling, B. F. Francis Ouellette:
Atlas - a data warehouse for integrative bioinformatics.
34
- Markus Neuhäuser, Tanja Boes, Karl-Heinz Jöckel:
Two-part permutation tests for DNA methylation and microarray data.
35
- Robert G. Beiko, Robert L. Charlebois:
GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA.
36
- Timothy Lu, Christine M. Costello, Peter J. P. Croucher, Robert Häsler, Günther Deuschl, Stefan Schreiber:
Can Zipf's law be adapted to normalize microarrays?
37
- Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang:
htSNPer1.0: software for haplotype block partition and htSNPs selection.
38
- Ruth Dunn, Frank Dudbridge, Christopher M. Sanderson:
The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks.
39
- Itay Tirosh, Naama Barkai:
Computational verification of protein-protein interactions by orthologous co-expression.
40
- Florent Angly, Beltran Rodriguez-Brito, David Bangor, Pat McNairnie, Mya Breitbart, Peter Salamon, Ben Felts, James Nulton, Joseph Mahaffy, Forest Rohwer:
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information.
41
- Julie Aubert, Avner Bar-Hen, Jean-Jacques Daudin, Stéphane Robin:
Correction: Determination of the differentially expressed genes in microarray experiments using local FDR.
42
- Koji Kadota, Ryutaro Fukumura, Joseph J. Rodrigue, Ryoko Araki, Masumi Abe:
A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: Toward the strict alignment of valid fragments across electrophoretic patterns.
43
- Wen-Chieh Chang, Chang-Wei Li, Bor-Sen Chen:
Quantitative inference of dynamic regulatory pathways via microarray data.
44
- John Colbourne, Vasanth R. Singan, Don G. Gilbert:
wFleaBase: the Daphnia genome database.
45
- Noam Kaplan, Michal Linial:
Automatic detection of false annotations via binary property clustering.
46
- Guangjie Feng, Nick Burton, Bill Hill, Duncan Davidson, Janet Kerwin, Mark Scott, Susan Lindsay, Richard A. Baldock:
JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.
47
- Roderic D. M. Page:
A Taxonomic Search Engine: Federating taxonomic databases using web services.
48
- Olivier Bastien, Philippe Ortet, Sylvaine Roy, Eric Maréchal:
A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.
49
- Eva Freyhult, Peteris Prusis, Maris Lapinsh, Jarl E. S. Wikberg, Vincent Moulton, Mats G. Gustafsson:
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling.
50
- Blaise T. F. Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster:
CoPub Mapper: mining MEDLINE based on search term co-publication.
51
- Siv Midtun Hollup, Gisle Sælensminde, Nathalie Reuter:
WEBnm@: a web application for normal mode analyses of proteins.
52
- Jaime E. Blair, Prachi Shah, S. Blair Hedges:
Evolutionary sequence analysis of complete eukaryote genomes.
53
- Harri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja, Wei Zhang:
In silico microdissection of microarray data from heterogeneous cell populations.
54
- Euan A. Adie, Richard R. Adams, Kathryn L. Evans, David J. Porteous, Ben S. Pickard:
Speeding disease gene discovery by sequence based candidate prioritization.
55
- Andrew G. Garrow, Alison Agnew, David R. Westhead:
TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins.
56
- John R. Stevens, R. W. Doerge:
Combining Affymetrix microarray results.
57
- Zheng Guo, Tianwen Zhang, Xia Li, Qi Wang, Jianzhen Xu, Hui Yu, Jing Zhu, Haiyun Wang, Chenguang Wang, Eric J. Topol, Qing Wang, Shaoqi Rao:
Towards precise classification of cancers based on robust gene functional expression profiles.
58
- Gajendra P. S. Raghava, Joon H. Han:
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein.
59
- Lin Wang, Simin Liu, Tianhua Niu, Xin Xu:
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
60
- Yadhu Kumar, Ralf Westram, Sebastian Behrens, Bernhard Fuchs, Frank Oliver Glöckner, Rudolf Amann, Harald Meier, Wolfgang Ludwig:
Graphical representation of ribosomal RNA probe accessibility data using ARB software package.
61
- Alexey Larionov, Andreas Krause, William Miller:
A standard curve based method for relative real time PCR data processing.
62
- Elena Rivas:
Evolutionary models for insertions and deletions in a probabilistic modeling framework.
63
- James J. Cai, David K. Smith, Xuhua Xia, Kwok-yung Yuen:
MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution.
64
- Mayte Suárez-Fariñas, Asifa Haider, Knut M. Wittkowski:
"Harshlighting" small blemishes on microarrays.
65
- Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern:
DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment.
66
- Li M. Fu, Casey S. Fu-Liu:
Evaluation of gene importance in microarray data based upon probability of selection.
67
- Ilya Levner:
Feature selection and nearest centroid classification for protein mass spectrometry.
68
- Francis Tang, Ching Lian Chua, Liang-Yoong Ho, Yun-Ping Lim, Praveen Issac, Arun Krishnan:
Wildfire: distributed, Grid-enabled workflow construction and execution.
69
- C. Titus Brown, Yuan Xie, Eric H. Davidson, R. Andrew Cameron:
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.
70
- Hartmut Scheel, Kay Hofmann:
Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes.
71
- S. A. Kirov, X. Peng, E. Baker, D. Schmoyer, B. Zhang, J. Snoddy:
GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments.
72
- Ian Holmes:
Accelerated probabilistic inference of RNA structure evolution.
73
- Aba-Sah Dadzie, Albert Burger:
Providing visualisation support for the analysis of anatomy ontology data.
74
- Brian P. Suomela, Miguel A. Andrade:
Ranking the whole MEDLINE database according to a large training set using text indexing.
75
- Xiaoxing Liu, Arun Krishnan, Adrian Mondry:
An Entropy-based gene selection method for cancer classification using microarray data.
76
- Ya Zhang, John-Marc Chandonia, Chris H. Q. Ding, Stephen R. Holbrook:
Comparative mapping of sequence-based and structure-based protein domains.
77
- Chris D. Bajdik, Byron Kuo, Shawn Rusaw, Steven Jones, Angela Brooks-Wilson:
CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.
78
- Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva:
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
79
- Alexander Ploner, Lance D. Miller, Per Hall, Jonas Bergh, Yudi Pawitan:
Correlation test to assess low-level processing of high-density oligonucleotide microarray data.
80
- Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser:
Columba: an integrated database of proteins, structures, and annotations.
81
- Igor V. Tetko, Axel Facius, Andreas Ruepp, Hans-Werner Mewes:
Super paramagnetic clustering of protein sequences.
82
- Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Jotun Hein:
Bayesian coestimation of phylogeny and sequence alignment.
83
- Markus T. Friberg, Peter von Rohr, Gaston H. Gonnet:
Scoring functions for transcription factor binding site prediction.
84
- Wei Chen, Fikret Erdogan, H.-Hilger Ropers, Steffen Lenzner, Reinhard Ullmann:
CGHPRO - A comprehensive data analysis tool for array CGH.
85
- Prinal Trivedi, Jode W. Edwards, Jelai Wang, Gary L. Gadbury, Vinodh Srinivasasainagendra, Stanislav O. Zakharkin, Kyoungmi Kim, Tapan Mehta, Jacob P. L. Brand, Amit Patki, Grier P. Page, David B. Allison:
HDBStat!: A platform-independent software suite for statistical analysis of high dimensional biology data.
86
- Alexander García Castro, Samuel Thoraval, Leyla Jael García-Castro, Mark A. Ragan:
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.
87
- Lei Shi, Fabien Campagne:
Building a protein name dictionary from full text: a machine learning term extraction approach.
88
- Jianghui Liu, Jason Tsong-Li Wang, Jun Hu, Bin Tian:
A method for aligning RNA secondary structures and its application to RNA motif detection.
89
- Mark J. Gibbs, John S. Armstrong, Adrian J. Gibbs:
Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences.
90
- Andreas Möglich, Daniel Weinfurtner, Till Maurer, Wolfram Gronwald, Hans Robert Kalbitzer:
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles.
91
- Le Sy Vinh, Arndt von Haeseler:
Shortest triplet clustering: reconstructing large phylogenies using representative sets.
92
- Scot E. Dowd, Joaquin Zaragoza, Javier R. Rodriguez, Melvin J. Oliver, Paxton R. Payton:
Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST).
93
- Nicole Donofrio, Ravi Rajagopalon, Douglas E. Brown, Stephen E. Diener, Donald Windham, Shelly Nolin, Anna Floyd, Thomas K. Mitchell, Natalia Galadima, Sara Tucker, Marc J. Orbach, Gayatri Patel, Mark L. Farman, Vishal Pampanwar, Cari Soderlund, Yong-Hwan Lee, Ralph A. Dean:
'PACLIMS': A component LIM system for high-throughput functional genomic analysis.
94
- Judith E. Stenger, Hong Xu, Carol Haynes, Elizabeth R. Hauser, Margaret A. Pericak-Vance, Pascal J. Goldschmidt-Clermont, Jeffery M. Vance:
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.
95
- Jeffrey P. Mower:
PREP-Mt: predictive RNA editor for plant mitochondrial genes.
96
- Leslie Grate:
Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery.
97
- Michael Watson:
ProGenExpress: Visualization of quantitative data on prokaryotic genomes.
98
- Markus Wistrand, Erik L. L. Sonnhammer:
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.
99
