Volume 8, issue 1, December 2007
488 articles in this issue
-
-
Weighted analysis of general microarray experiments
Authors (first, second and last of 4)
- Anders Sjögren
- Erik Kristiansson
- Olle Nerman
- Content type: Methodology article
- Open Access
- Published: 15 October 2007
- Article: 387
-
Large scale statistical inference of signaling pathways from RNAi and microarray data
Authors (first, second and last of 5)
- Holger Froehlich
- Mark Fellmann
- Tim Beissbarth
- Content type: Research article
- Open Access
- Published: 15 October 2007
- Article: 386
-
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm
Authors
- Emma Redhead
- Timothy L Bailey
- Content type: Research article
- Open Access
- Published: 15 October 2007
- Article: 385
-
Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling
Authors
- Yung-Keun Kwon
- Sun Shim Choi
- Kwang-Hyun Cho
- Content type: Research article
- Open Access
- Published: 15 October 2007
- Article: 384
-
ProbCD: enrichment analysis accounting for categorization uncertainty
Authors
- Ricardo ZN Vêncio
- Ilya Shmulevich
- Content type: Software
- Open Access
- Published: 12 October 2007
- Article: 383
-
XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences
Authors
- Aaron M Newman
- James B Cooper
- Content type: Software
- Open Access
- Published: 11 October 2007
- Article: 382
-
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
Authors (first, second and last of 10)
- Daniel R Caffrey
- Paul H Dana
- Enoch S Huang
- Content type: Software
- Open Access
- Published: 11 October 2007
- Article: 381
-
Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots
Authors
- Oliviero Carugo
- Content type: Methodology article
- Open Access
- Published: 11 October 2007
- Article: 380
-
RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses
Authors
- Dianhui Zhu
- George E Fox
- Sugoto Chakravarty
- Content type: Software
- Open Access
- Published: 10 October 2007
- Article: 379
-
Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella
Authors (first, second and last of 8)
- William O Ward
- Carol D Swartz
- David M DeMarini
- Content type: Research article
- Open Access
- Published: 09 October 2007
- Article: 378
-
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies
Authors (first, second and last of 4)
- Robert Hoehndorf
- Frank Loebe
- Heinrich Herre
- Content type: Methodology article
- Open Access
- Published: 09 October 2007
- Article: 377
-
Single TNFα trimers mediating NF-κ B activation: stochastic robustness of NF-κ B signaling
Authors (first, second and last of 5)
- Tomasz Lipniacki
- Krzysztof Puszynski
- Marek Kimmel
- Content type: Research article
- Open Access
- Published: 09 October 2007
- Article: 376
-
Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid
Authors (first, second and last of 5)
- Bingjun Jiang
- Hong Qu
- Zhongping Lin
- Content type: Research article
- Open Access
- Published: 09 October 2007
- Article: 375
-
Statistical power of phylo-HMM for evolutionarily conserved element detection
Authors (first, second and last of 4)
- Xiaodan Fan
- Jun Zhu
- Jun S Liu
- Content type: Research article
- Open Access
- Published: 05 October 2007
- Article: 374
-
qPIPSA: Relating enzymatic kinetic parameters and interaction fields
Authors
- Razif R Gabdoulline
- Matthias Stein
- Rebecca C Wade
- Content type: Research article
- Open Access
- Published: 05 October 2007
- Article: 373
-
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases
Authors
- Seth I Berger
- Jeremy M Posner
- Avi Ma'ayan
- Content type: Software
- Open Access
- Published: 04 October 2007
- Article: 372
-
Extended analysis of benchmark datasets for Agilent two-color microarrays
Authors
- Kathleen F Kerr
- Content type: Methodology article
- Open Access
- Published: 03 October 2007
- Article: 371
-
Gene selection for classification of microarray data based on the Bayes error
Authors
- Ji-Gang Zhang
- Hong-Wen Deng
- Content type: Methodology article
- Open Access
- Published: 03 October 2007
- Article: 370
-
Primique: automatic design of specific PCR primers for each sequence in a family
Authors
- Jakob Fredslund
- Mette Lange
- Content type: Software
- Open Access
- Published: 03 October 2007
- Article: 369
-
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data
Authors (first, second and last of 19)
- Ágnes Baross
- Allen D Delaney
- Marco A Marra
- Content type: Research article
- Open Access
- Published: 02 October 2007
- Article: 368
-
BNDB – The Biochemical Network Database
Authors (first, second and last of 7)
- Jan Küntzer
- Christina Backes
- Hans-Peter Lenhof
- Content type: Database
- Open Access
- Published: 02 October 2007
- Article: 367
-
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules
Authors (first, second and last of 4)
- Yair Horesh
- Tirza Doniger
- Ron Unger
- Content type: Methodology article
- Open Access
- Published: 01 October 2007
- Article: 366
-
Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype
Authors (first, second and last of 4)
- Israel M Martínez-Pérez
- Gong Zhang
- Karl-Heinz Zimmermann
- Content type: Research article
- Open Access
- Published: 28 September 2007
- Article: 365
-
A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments
Authors (first, second and last of 4)
- Hyungwon Choi
- Ronglai Shen
- Debashis Ghosh
- Content type: Methodology article
- Open Access
- Published: 27 September 2007
- Article: 364
-
Estimation of the number of extreme pathways for metabolic networks
Authors
- Matthew Yeung
- Ines Thiele
- Bernard Ø Palsson
- Content type: Research article
- Open Access
- Published: 27 September 2007
- Article: 363
-
Design and implementation of a generalized laboratory data model
Authors (first, second and last of 14)
- Michael C Wendl
- Scott Smith
- Richard K Wilson
- Content type: Methodology article
- Open Access
- Published: 26 September 2007
- Article: 362
-
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines
Authors (first, second and last of 5)
- Huynh-Hoa Bui
- John Sidney
- Alessandro Sette
- Content type: Software
- Open Access
- Published: 26 September 2007
- Article: 361
-
Linking microarray reporters with protein functions
Authors (first, second and last of 4)
- Stan Gaj
- Arie van Erk
- Chris TA Evelo
- Content type: Methodology article
- Open Access
- Published: 26 September 2007
- Article: 360
-
Differential analysis for high density tiling microarray data
Authors (first, second and last of 6)
- Srinka Ghosh
- Heather A Hirsch
- Thomas R Gingeras
- Content type: Methodology article
- Open Access
- Published: 24 September 2007
- Article: 359
-
Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements
Authors (first, second and last of 4)
- Hui Lan
- Rachel Carson
- Anthony J Bonner
- Content type: Research article
- Open Access
- Published: 21 September 2007
- Article: 358
-
An evolutionary method for learning HMM structure: prediction of protein secondary structure
Authors (first, second and last of 4)
- Kyoung-Jae Won
- Thomas Hamelryck
- Anders Krogh
- Content type: Research article
- Open Access
- Published: 21 September 2007
- Article: 357
-
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
Authors
- Jos Boekhorst
- Berend Snel
- Content type: Research article
- Open Access
- Published: 21 September 2007
- Article: 356
-
Accuracy of structure-based sequence alignment of automatic methods
Authors
- Changhoon Kim
- Byungkook Lee
- Content type: Research article
- Open Access
- Published: 20 September 2007
- Article: 355
-
SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences
Authors
- Fathi Elloumi
- Martha Nason
- Content type: Methodology article
- Open Access
- Published: 20 September 2007
- Article: 354
-
Prediction of potential drug targets based on simple sequence properties
Authors
- Qingliang Li
- Luhua Lai
- Content type: Research article
- Open Access
- Published: 20 September 2007
- Article: 353
-
Tandem mass spectrometry data quality assessment by self-convolution
Authors
- Keng Wah Choo
- Wai Mun Tham
- Content type: Methodology article
- Open Access
- Published: 20 September 2007
- Article: 352
-
A machine learning approach for the identification of odorant binding proteins from sequence-derived properties
Authors (first, second and last of 5)
- Ganesan Pugalenthi
- Ke Tang
- R Sowdhamini
- Content type: Research article
- Open Access
- Published: 19 September 2007
- Article: 351
-
Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy
Authors (first, second and last of 5)
- Guangan Hu
- Manuel Llinás
- Zbynek Bozdech
- Content type: Methodology article
- Open Access
- Published: 19 September 2007
- Article: 350
-
A cross-species alignment tool (CAT)
Authors (first, second and last of 7)
- Heng Li
- Liang Guan
- Jun Wang
- Content type: Methodology article
- Open Access
- Published: 19 September 2007
- Article: 349
-
PADB : Published Association Database
Authors
- Hwanseok Rhee
- Jin-Sung Lee
- Content type: Database
- Open Access
- Published: 19 September 2007
- Article: 348
-
A unified framework for finding differentially expressed genes from microarray experiments
Authors
- Jahangheer S Shaik
- Mohammed Yeasin
- Content type: Research article
- Open Access
- Published: 18 September 2007
- Article: 347
-
A framework for significance analysis of gene expression data using dimension reduction methods
Authors (first, second and last of 4)
- Lars Gidskehaug
- Endre Anderssen
- Bjørn K Alsberg
- Content type: Research article
- Open Access
- Published: 18 September 2007
- Article: 346
-
Benchmarking consensus model quality assessment for protein fold recognition
Authors
- Liam J McGuffin
- Content type: Research article
- Open Access
- Published: 18 September 2007
- Article: 345
-
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context
Authors (first, second and last of 4)
- Jeremiah J Faith
- Andrew J Olson
- Ravi Sachidanandam
- Content type: Software
- Open Access
- Published: 18 September 2007
- Article: 344
-
Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model
Authors (first, second and last of 6)
- Ryoko Morioka
- Shigehiko Kanaya
- Kazuki Saito
- Content type: Research article
- Open Access
- Published: 18 September 2007
- Article: 343
-
A replica exchange Monte Carlo algorithm for protein folding in the HP model
Authors
- Chris Thachuk
- Alena Shmygelska
- Holger H Hoos
- Content type: Research article
- Open Access
- Published: 17 September 2007
- Article: 342
-
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans
Authors (first, second and last of 6)
- Ting-Hua Huang
- Bin Fan
- Shu-Hong Zhao
- Content type: Software
- Open Access
- Published: 17 September 2007
- Article: 341
-
Impact of image segmentation on high-content screening data quality for SK-BR-3 cells
Authors (first, second and last of 4)
- Andrew A Hill
- Peter LaPan
- Steve Haney
- Content type: Research article
- Open Access
- Published: 14 September 2007
- Article: 340
-
A Bayesian nonparametric method for prediction in EST analysis
Authors
- Antonio Lijoi
- Ramsés H Mena
- Igor Prünster
- Content type: Methodology article
- Open Access
- Published: 14 September 2007
- Article: 339