Liisa Holm

PLoS Comput. Biol., 2022

Dali server: structural unification of protein families.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2022

2021

A New Approach to Multilabel Stratified Cross Validation with Application to Large and Sparse Gene Ontology Datasets.

[BibT_eX]

[DOI]

Henri Tiittanen

CoRR, 2021

2019

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2019

Benchmarking fold detection by DaliLite v.5.

[BibT_eX]

[DOI]

Bioinform., 2019

2018

PANNZER2: a rapid functional annotation web server.

[BibT_eX]

[DOI]

Alan Medlar

Nucleic Acids Res., 2018

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.

[BibT_eX]

[DOI]

Alan Medlar

Nucleic Acids Res., 2018

Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search.

[BibT_eX]

[DOI]

Reda Younsi

Jing Tang

CoRR, 2018

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.

[BibT_eX]

[DOI]

BMC Bioinform., 2018

TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases.

[BibT_eX]

[DOI]

Alan Medlar

BMC Bioinform., 2018

2016

Dali server update.

[BibT_eX]

[DOI]

Laura M. Laakso

Nucleic Acids Res., 2016

Robust multi-group gene set analysis with few replicates.

[BibT_eX]

[DOI]

BMC Bioinform., 2016

2015

SANSparallel: interactive homology search against Uniprot.

[BibT_eX]

[DOI]

Panu Somervuo

Nucleic Acids Res., 2015

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.

[BibT_eX]

[DOI]

Bioinform., 2015

2014

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2014

Pfam: the protein families database.

[BibT_eX]

[DOI]

Erik L. L. Sonnhammer

John G. Tate

Marco Punta

Nucleic Acids Res., 2014

Gene set analysis: limitations in popular existing methods and proposed improvements.

[BibT_eX]

[DOI]

Bioinform., 2014

2013

GOParGenPy: a high throughput method to generate Gene Ontology data matrices.

[BibT_eX]

[DOI]

Ajay Kumar

BMC Bioinform., 2013

2012

The Pfam protein families database.

[BibT_eX]

[DOI]

Erik L. L. Sonnhammer

Sean R. Eddy

Alex Bateman

Robert D. Finn

Nucleic Acids Res., 2012

Comprehensive comparison of graph based multiple protein sequence alignment strategies.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.

[BibT_eX]

[DOI]

Teija Ojala

BMC Bioinform., 2012

SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.

[BibT_eX]

[DOI]

Patrik Koskinen

Bioinform., 2012

2011

A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees.

[BibT_eX]

[DOI]

Hung Xuan Ta

Patrik Koskinen

Bioinform., 2011

MPEA - metabolite pathway enrichment analysis.

[BibT_eX]

[DOI]

Peddinti V. Gopalacharyulu

Matej Oresic

Bioinform., 2011

2010

Dali server: conservation mapping in 3D.

[BibT_eX]

[DOI]

Päivi Rosenström

Nucleic Acids Res., 2010

The Pfam protein families database.

[BibT_eX]

[DOI]

Erik L. L. Sonnhammer

Sean R. Eddy

Alex Bateman

Nucleic Acids Res., 2010

Inferring the physical connectivity of complex networks from their functional dynamics.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2010

Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function.

[BibT_eX]

Proceedings of the BIOINFORMATICS 2010, 2010

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels.

[BibT_eX]

[DOI]

Proceedings of the Biomedical Engineering Systems and Technologies, 2010

2009

Generation of Gene Ontology benchmark datasets with various types of positive signal.

[BibT_eX]

[DOI]

Petri Pehkonen

BMC Bioinform., 2009

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.

[BibT_eX]

[DOI]

BMC Bioinform., 2009

LOCP - locating pilus operons in Gram-positive bacteria.

[BibT_eX]

[DOI]

Bioinform., 2009

Evaluation of Novel Protein Structure Comparison Algorithms Based on Objective Function Rankings.

[BibT_eX]

[DOI]

Hitomi Hasegawa

Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics, 2009

2008

PairsDB atlas of protein sequence space.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2008

Searching protein structure databases with DaliLite v.3.

[BibT_eX]

[DOI]

Bioinform., 2008

2007

The global trace graph, a novel paradigm for searching protein sequence databases.

[BibT_eX]

[DOI]

Christopher Andrew Wilton

Swapan Mallick

Bioinform., 2007

2006

POXO: a web-enabled tool series to discover transcription factor binding sites.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2006

Bayesian search of functionally divergent protein subgroups and their function specific residues.

[BibT_eX]

[DOI]

Bioinform., 2006

2005

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2005

ADDA: a domain database with global coverage of the protein universe.

[BibT_eX]

[DOI]

Christopher Andrew Wilton

Ashwin Sivakumar

Nucleic Acids Res., 2005

PSIbase: a database of Protein Structural Interactome map (PSIMAP).

[BibT_eX]

[DOI]

Bioinform., 2005

2004

POBO, transcription factor binding site verification with bootstrapping.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2004

Accurate Detection of Very Sparse Sequence Motifs.

[BibT_eX]

[DOI]

Michael Lappe

J. Comput. Biol., 2004

2003

Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins.

[BibT_eX]

[DOI]

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2001

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2001

Picasso: generating a covering set of protein family profiles.

[BibT_eX]

[DOI]

Bioinform., 2001

Generating protein interaction maps from incomplete data: application to fold assignment.

[BibT_eX]

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000

RSDB: representative protein sequence databases have high information content.

[BibT_eX]

[DOI]

Bioinform., 2000

Sequence search algorithm assessment and testing toolkit (SAT).

[BibT_eX]

[DOI]

Jong-Chan Park

Cyrus Chothia

Bioinform., 2000

Estimating the significance of sequence order in protein secondary structure and prediction.

[BibT_eX]

[DOI]

Bioinform., 2000

DaliLite workbench for protein structure comparison.

[BibT_eX]

[DOI]

Jong-Chan Park

Bioinform., 2000

1999

Protein folds and families: sequence and structure alignments.

[BibT_eX]

[DOI]

Nucleic Acids Res., 1999

1998

Touring protein fold space with Dali/FSSP.

[BibT_eX]

[DOI]

Nucleic Acids Res., 1998

COFFEE: an objective function for multiple sequence alignments.

[BibT_eX]

[DOI]

Cédric Notredame

Desmond G. Higgins

Bioinform., 1998

Removing near-neighbour redundancy from large protein sequence collections.

[BibT_eX]

[DOI]

Bioinform., 1998

1997

Dali/FSSP classification of three-dimensional protein folds.

[BibT_eX]

[DOI]

Nucleic Acids Res., 1997

Decision Support System for the Evolutionary Classification of Protein Structures.

[BibT_eX]

[DOI]

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

1996

The FSSP database: fold classification based on structure-structure alignment of proteins.

[BibT_eX]

[DOI]

Nucleic Acids Res., 1996

1995

3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability.

[BibT_eX]

[DOI]