Liisa Holm

Orcid: 0000-0002-7807-2966

According to our database1, Liisa Holm authored at least 59 papers between 1995 and 2022.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

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PhD thesis 
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Links

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Bibliography

2022
Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
PLoS Comput. Biol., 2022

Dali server: structural unification of protein families.
Nucleic Acids Res., 2022

2021
A New Approach to Multilabel Stratified Cross Validation with Application to Large and Sparse Gene Ontology Datasets.
CoRR, 2021

2019
Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
PLoS Comput. Biol., 2019

Benchmarking fold detection by DaliLite v.5.
Bioinform., 2019

2018
PANNZER2: a rapid functional annotation web server.
Nucleic Acids Res., 2018

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.
Nucleic Acids Res., 2018

Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search.
CoRR, 2018

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.
BMC Bioinform., 2018

TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases.
BMC Bioinform., 2018

2016
Dali server update.
Nucleic Acids Res., 2016

Robust multi-group gene set analysis with few replicates.
BMC Bioinform., 2016

2015
SANSparallel: interactive homology search against Uniprot.
Nucleic Acids Res., 2015

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.
Bioinform., 2015

2014
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.
PLoS Comput. Biol., 2014

Pfam: the protein families database.
Nucleic Acids Res., 2014

Gene set analysis: limitations in popular existing methods and proposed improvements.
Bioinform., 2014

2013
GOParGenPy: a high throughput method to generate Gene Ontology data matrices.
BMC Bioinform., 2013

2012
The Pfam protein families database.
Nucleic Acids Res., 2012

Comprehensive comparison of graph based multiple protein sequence alignment strategies.
BMC Bioinform., 2012

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.
BMC Bioinform., 2012

SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.
Bioinform., 2012

2011
A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees.
Bioinform., 2011

MPEA - metabolite pathway enrichment analysis.
Bioinform., 2011

2010
Dali server: conservation mapping in 3D.
Nucleic Acids Res., 2010

The Pfam protein families database.
Nucleic Acids Res., 2010

Inferring the physical connectivity of complex networks from their functional dynamics.
BMC Syst. Biol., 2010

Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function.
Proceedings of the BIOINFORMATICS 2010, 2010

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels.
Proceedings of the Biomedical Engineering Systems and Technologies, 2010

2009
Generation of Gene Ontology benchmark datasets with various types of positive signal.
BMC Bioinform., 2009

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.
BMC Bioinform., 2009

LOCP - locating pilus operons in Gram-positive bacteria.
Bioinform., 2009

Evaluation of Novel Protein Structure Comparison Algorithms Based on Objective Function Rankings.
Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics, 2009

2008
PairsDB atlas of protein sequence space.
Nucleic Acids Res., 2008

Searching protein structure databases with DaliLite v.3.
Bioinform., 2008

2007
The global trace graph, a novel paradigm for searching protein sequence databases.
Bioinform., 2007

2006
POXO: a web-enabled tool series to discover transcription factor binding sites.
Nucleic Acids Res., 2006

Bayesian search of functionally divergent protein subgroups and their function specific residues.
Bioinform., 2006

2005
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.
Nucleic Acids Res., 2005

ADDA: a domain database with global coverage of the protein universe.
Nucleic Acids Res., 2005

PSIbase: a database of Protein Structural Interactome map (PSIMAP).
Bioinform., 2005

2004
POBO, transcription factor binding site verification with bootstrapping.
Nucleic Acids Res., 2004

Accurate Detection of Very Sparse Sequence Motifs.
J. Comput. Biol., 2004

2003
Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins.
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.
Nucleic Acids Res., 2001

Picasso: generating a covering set of protein family profiles.
Bioinform., 2001

Generating protein interaction maps from incomplete data: application to fold assignment.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000
RSDB: representative protein sequence databases have high information content.
Bioinform., 2000

Sequence search algorithm assessment and testing toolkit (SAT).
Bioinform., 2000

Estimating the significance of sequence order in protein secondary structure and prediction.
Bioinform., 2000

DaliLite workbench for protein structure comparison.
Bioinform., 2000

1999
Protein folds and families: sequence and structure alignments.
Nucleic Acids Res., 1999

1998
Touring protein fold space with Dali/FSSP.
Nucleic Acids Res., 1998

COFFEE: an objective function for multiple sequence alignments.
Bioinform., 1998

Removing near-neighbour redundancy from large protein sequence collections.
Bioinform., 1998

1997
Dali/FSSP classification of three-dimensional protein folds.
Nucleic Acids Res., 1997

Decision Support System for the Evolutionary Classification of Protein Structures.
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.
Nucleic Acids Res., 1996

1995
3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995


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