Headings in this document
1. Nature Protocols (Peer-reviewed part of our content)
2. Network Protocols (Open access part of our content)
3. In the pipeline and ideas


1. Nature Protocols (Peer-reviewed part of our content)

Locating potential enhancer elements by comparative genomics using the EEL software
http://www.nature.com/nprot/journal/v1/n1/abs/nprot.2006.56.html

The mode-of-action by network identification (MNI) algorithm: a network biology approach for molecular target identification

Reverse engineering cellular networks
http://www.nature.com/nprot/journal/v1/n2/abs/nprot.2006.106.html

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
http://www.nature.com/nprot/journal/v2/n3/abs/nprot.2007.99.html

Locating proteins in the cell using TargetP, SignalP and related tools
http://www.nature.com/nprot/journal/v2/n4/abs/nprot.2007.131.html

A general user interface for prediction servers of proteins' post-translational modification sites
http://www.nature.com/nprot/journal/v1/n3/abs/nprot.2006.209.html

Analysis and interpretation of quadratic models of receptive fields
http://www.nature.com/nprot/journal/v2/n2/abs/nprot.2007.27.html

Identification and insertion of 3-carbon bridges in protein disulfide bonds: a computational approach
http://www.nature.com/nprot/journal/v2/n5/abs/nprot.2007.119.html

Probe Selection for DNA Microarrays using OligoWiz
[Accepted, but not published]

Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
http://www.nature.com/nprot/journal/v3/n2/abs/nprot.2007.494.html

 

Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts
http://www.nature.com/nprot/journal/v2/n11/abs/nprot.2007.376.html

 

Version 1.2 of the Crystallography and NMR system
http://www.nature.com/nprot/journal/v2/n11/abs/nprot.2007.406.html

 

Integration of biological networks and gene expression data using Cytoscape
http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.324.html

 

Patent searches as a complement to literature searches in the life sciences—a 'how-to' tutorial
http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.355.html





2. Network Protocols (Open access part of our content)

BaCelLo: a Balanced subCellular Localization predictor.
http://www.natureprotocols.com/2007/03/13/bacello_a_balanced_subcellular.php

Large Scale Vitreous Fluid Proteomics using 1D SDS-PAGE, Tandem Mass Spectrometry, and a Relational Database.
http://www.natureprotocols.com/2007/03/08/large_scale_vitreous_fluid_pro.php

AFPredictor: A computational screening protocol for antifreeze/ice-structuring proteins
http://www.natureprotocols.com/2006/08/17/afpredictor_a_computational_sc.php

A Novel Method for Site-determination of Tyrosine O-sulfation in Peptides and Proteins
http://www.natureprotocols.com/2007/09/20/a_novel_method_for_sitedetermi.php

Investigating patchiness of spatially organized ecosystems using field and simulated data
http://www.natureprotocols.com/2007/09/17/investigating_patchiness_of_sp.php

GPS: A computational protocol for kinase-specific phosphorylation site prediction
http://www.natureprotocols.com/2007/05/11/gps_a_computational_protocol_f.php

A practical efficient approach in high throughput screening: using FDR and fold change
http://www.natureprotocols.com/2007/04/16/a_practical_efficient_approach.php

Assembly of the highly similar sequences of the IS elements by the means of phrap and miniassembly maker perl scripts
http://www.natureprotocols.com/2007/03/22/assembly_of_the_highly_similar.php

Large Scale Vitreous Fluid Proteomics using 1D SDS-PAGE, Tandem Mass Spectrometry, and a Relational Database
http://www.natureprotocols.com/2007/03/08/large_scale_vitreous_fluid_pro.php




3. In the pipeline and ideas

Molecular evolutionary analysis using MEGA software

Bayesian phylogenetic inference using MrBayes software

Homology modelling of protein structures using SWISS-MODEL

Regulatory Sequence Analysis (RSA) Tools (RSAT) - series of modular porgrams specifically designed for detecting regulatory signals in non-coding sequences. http://rsat.scmbb.ulb.ac.be/rsat/

Significance Analysis of Microarrays (SAM), that assigns a score to each gene on the basis of change in gene expression relative to the standard deviation of repeated measurements

NucPred - predicting nuclear localisation of proteins

3DNA

Visualizing and exploring genomic information for non protein coding identification using ApolloRNA

A bioinformatics approach to predict host-pathogen protein-protein interactions

SPIDER manual

Molecular evolutionary analysis using MEGA software