Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets

Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks

(2014) Inhae Kim et al.   PLoS Computational Biology

Dissemination of scientific software with Galaxy ToolShed

(2014) Daniel Blankenberg et al.   GENOME BIOLOGY

The eukaryotic linear motif resource ELM: 10 years and counting

(2013) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

(2012) Massimo Andreatta et al.   BIOINFORMATICS

Deep sequencing analysis of phage libraries using Illumina platform

(2012) Wadim L. Matochko et al.   METHODS

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets

(2012) TaeHyung Kim et al.   NUCLEIC ACIDS RESEARCH

The multiple-specificity landscape of modular peptide recognition domains

(2011) D. Gfeller et al.   Molecular Systems Biology

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Diversity of Phage-Displayed Libraries of Peptides during Panning and Amplification

(2011) Ratmir Derda et al.   MOLECULES

Bioinformatics Resources and Tools for Phage Display

(2011) Jian Huang et al.   MOLECULES

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

(2011) Massimo Andreatta et al.   PLoS One

A general method for characterization of humoral immunity induced by a vaccine or infection

(2010) Joseph Barten Legutki et al.   VACCINE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

(2009) Morten Nielsen et al.   BMC BIOINFORMATICS

Progress in phage display: evolution of the technique and its applications

(2009) Tomaž Bratkovič   CELLULAR AND MOLECULAR LIFE SCIENCES