Volume 8, issue 1, December 2007
488 articles in this issue
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Boolean networks using the chi-square test for inferring large-scale gene regulatory networks
Authors
- Haseong Kim
- Jae K Lee
- Taesung Park
- Content type: Methodology article
- Open Access
- Published: 01 February 2007
- Article: 37
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GEVALT: An integrated software tool for genotype analysis
Authors
- Ofir Davidovich
- Gad Kimmel
- Ron Shamir
- Content type: Software
- Open Access
- Published: 01 February 2007
- Article: 36
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Classification of microarray data using gene networks
Authors (first, second and last of 5)
- Franck Rapaport
- Andrei Zinovyev
- Jean-Philippe Vert
- Content type: Research article
- Open Access
- Published: 01 February 2007
- Article: 35
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Computational RNA secondary structure design: empirical complexity and improved methods
Authors
- RosalÃa Aguirre-Hernández
- Holger H Hoos
- Anne Condon
- Content type: Research article
- Open Access
- Published: 31 January 2007
- Article: 34
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Considerations in the identification of functional RNA structural elements in genomic alignments
Authors
- Tomas Babak
- Benjamin J Blencowe
- Timothy R Hughes
- Content type: Research article
- Open Access
- Published: 30 January 2007
- Article: 33
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Context based mixture model for cell phase identification in automated fluorescence microscopy
Authors (first, second and last of 4)
- Meng Wang
- Xiaobo Zhou
- Stephen TC Wong
- Content type: Research article
- Open Access
- Published: 30 January 2007
- Article: 32
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Conceptual-level workflow modeling of scientific experiments using NMR as a case study
Authors
- Kacy K Verdi
- Heidi JC Ellis
- Michael R Gryk
- Content type: Methodology article
- Open Access
- Published: 30 January 2007
- Article: 31
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Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control
Authors (first, second and last of 5)
- Ana P Teixeira
- Carlos Alves
- Rui Oliveira
- Content type: Methodology article
- Open Access
- Published: 29 January 2007
- Article: 30
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Measuring similarities between gene expression profiles through new data transformations
Authors (first, second and last of 7)
- Kyungpil Kim
- Shibo Zhang
- Haiyan Huang
- Content type: Research article
- Open Access
- Published: 27 January 2007
- Article: 29
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Detecting differential expression in microarray data: comparison of optimal procedures
Authors (first, second and last of 4)
- Elena Perelman
- Alexander Ploner
- Yudi Pawitan
- Content type: Research article
- Open Access
- Published: 26 January 2007
- Article: 28
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Scoring functions and enrichment: a case study on Hsp90
Authors
- Chrysi Konstantinou-Kirtay
- John BO Mitchell
- James A Lumley
- Content type: Research article
- Open Access
- Published: 26 January 2007
- Article: 27
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Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data
Authors (first, second and last of 5)
- Andy G Lynch
- David E Neal
- Natalie P Thorne
- Content type: Research article
- Open Access
- Published: 25 January 2007
- Article: 26
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Bias in random forest variable importance measures: Illustrations, sources and a solution
Authors (first, second and last of 4)
- Carolin Strobl
- Anne-Laure Boulesteix
- Torsten Hothorn
- Content type: Methodology article
- Open Access
- Published: 25 January 2007
- Article: 25
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Benchmarking natural-language parsers for biological applications using dependency graphs
Authors
- Andrew B Clegg
- Adrian J Shepherd
- Content type: Research article
- Open Access
- Published: 25 January 2007
- Article: 24
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Motif kernel generated by genetic programming improves remote homology and fold detection
Authors
- Tony HÃ¥ndstad
- Arne JH Hestnes
- Pål Sætrom
- Content type: Research article
- Open Access
- Published: 25 January 2007
- Article: 23
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Gene network interconnectedness and the generalized topological overlap measure
Authors
- Andy M Yip
- Steve Horvath
- Content type: Research article
- Open Access
- Published: 24 January 2007
- Article: 22
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GraphDNA: a Java program for graphical display of DNA composition analyses
Authors (first, second and last of 5)
- Jamie M Thomas
- Daniel Horspool
- Chris Upton
- Content type: Software
- Open Access
- Published: 23 January 2007
- Article: 21
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Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory
Authors
- Abdallah Sayyed-Ahmad
- Kagan Tuncay
- Peter J Ortoleva
- Content type: Research article
- Open Access
- Published: 23 January 2007
- Article: 20
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Statistical significance of cis-regulatory modules
Authors
- Dustin E Schones
- Andrew D Smith
- Michael Q Zhang
- Content type: Methodology article
- Open Access
- Published: 22 January 2007
- Article: 19
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PILER-CR: Fast and accurate identification of CRISPR repeats
Authors
- Robert C Edgar
- Content type: Software
- Open Access
- Published: 20 January 2007
- Article: 18
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Publishing perishing? Towards tomorrow's information architecture
Authors
- Michael R Seringhaus
- Mark B Gerstein
- Content type: Commentary
- Open Access
- Published: 19 January 2007
- Article: 17
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Multivariate Analysis and Visualization of Splicing Correlations in Single-Gene Transcriptomes
Authors
- Mark C Emerick
- Giovanni Parmigiani
- William S Agnew
- Content type: Methodology article
- Open Access
- Published: 18 January 2007
- Article: 16
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AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction
Authors (first, second and last of 8)
- Ayumu Saito
- Masao Nagasaki
- Satoru Miyano
- Content type: Software
- Open Access
- Published: 18 January 2007
- Article: 15
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Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation
Authors (first, second and last of 8)
- Rob Jelier
- Guido Jenster
- Jan A Kors
- Content type: Research article
- Open Access
- Published: 18 January 2007
- Article: 14
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Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
Authors
- Maria A Stalteri
- Andrew P Harrison
- Content type: Research article
- Open Access
- Published: 15 January 2007
- Article: 13
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Efficient classification of complete parameter regions based on semidefinite programming
Authors
- Lars Kuepfer
- Uwe Sauer
- Pablo A Parrilo
- Content type: Methodology article
- Open Access
- Published: 15 January 2007
- Article: 12
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In silico panning for a non-competitive peptide inhibitor
Authors (first, second and last of 5)
- Yukiko Yagi
- Kotaro Terada
- Koji Sode
- Content type: Research article
- Open Access
- Published: 12 January 2007
- Article: 11
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Bioinformatics analysis of the early inflammatory response in a rat thermal injury model
Authors (first, second and last of 5)
- Eric Yang
- Timothy Maguire
- Ioannis P Androulakis
- Content type: Methodology article
- Open Access
- Published: 10 January 2007
- Article: 10
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IDconverter and IDClight: Conversion and annotation of gene and protein IDs
Authors (first, second and last of 4)
- Andreu Alibés
- Patricio Yankilevich
- Ramón DÃaz-Uriarte
- Content type: Software
- Open Access
- Published: 10 January 2007
- Article: 9
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Least-squares methods for identifying biochemical regulatory networks from noisy measurements
Authors (first, second and last of 5)
- Jongrae Kim
- Declan G Bates
- Kwang-Hyun Cho
- Content type: Methodology article
- Open Access
- Published: 10 January 2007
- Article: 8
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eQTL Viewer: visualizing how sequence variation affects genome-wide transcription
Authors
- Wei Zou
- David L Aylor
- Zhao-Bang Zeng
- Content type: Software
- Open Access
- Published: 09 January 2007
- Article: 7
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Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
Authors
- Roger A Craig
- Li Liao
- Content type: Research article
- Open Access
- Published: 09 January 2007
- Article: 6
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Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering
Authors (first, second and last of 4)
- Nikhil R Pal
- Kripamoy Aguan
- Shun-ichi Amari
- Content type: Research article
- Open Access
- Published: 06 January 2007
- Article: 5
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VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines
Authors
- Irini A Doytchinova
- Darren R Flower
- Content type: Methodology article
- Open Access
- Published: 05 January 2007
- Article: 4
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FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data
Authors
- Limin Fu
- Enzo Medico
- Content type: Methodology article
- Open Access
- Published: 04 January 2007
- Article: 3
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TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences
Authors
- Manjunatha R Karpenahalli
- Andrei N Lupas
- Johannes Söding
- Content type: Software
- Open Access
- Published: 03 January 2007
- Article: 2
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Comparing sequences without using alignments: application to HIV/SIV subtyping
Authors (first, second and last of 7)
- Gilles Didier
- Laurent Debomy
- Ivan Laprevotte
- Content type: Research article
- Open Access
- Published: 02 January 2007
- Article: 1