3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability. - Liisa Holm; Chris Sander (ISMB, 1995)

The FSSP database: fold classification based on structure-structure alignment of proteins. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1996)

Decision Support System for the Evolutionary Classification of Protein Structures. - Liisa Holm; Chris Sander (ISMB, 1997)

Dali/FSSP classification of three-dimensional protein folds. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1997)

Removing near-neighbour redundancy from large protein sequence collections. - Liisa Holm; Chris Sander (Bioinform., 1998)

COFFEE: an objective function for multiple sequence alignments. - Cédric Notredame; Liisa Holm; Desmond G. Higgins (Bioinform., 1998)

Touring protein fold space with Dali/FSSP. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1998)

Protein folds and families: sequence and structure alignments. - Liisa Holm; Chris Sander (Nucleic Acids Res., 1999)

DaliLite workbench for protein structure comparison. - Liisa Holm; Jong-Chan Park (Bioinform., 2000)

Estimating the significance of sequence order in protein secondary structure and prediction. - Jong-Chan Park; Sabine Dietmann; Andreas Heger; Liisa Holm (Bioinform., 2000)

Sequence search algorithm assessment and testing toolkit (SAT). - Jong-Chan Park; Liisa Holm; Cyrus Chothia (Bioinform., 2000)

RSDB: representative protein sequence databases have high information content. - Jong-Chan Park; Liisa Holm; Andreas Heger; Cyrus Chothia (Bioinform., 2000)

Generating protein interaction maps from incomplete data: application to fold assignment. - Michael Lappe; Jong-Chan Park; Oliver Niggemann; Liisa Holm (ISMB (Supplement of Bioinformatics), 2001)

Picasso: generating a covering set of protein family profiles. - Andreas Heger; Liisa Holm (Bioinform., 2001)

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. - Sabine Dietmann; Jong-Chan Park; Cédric Notredame; Andreas Heger; Michael Lappe; Liisa Holm (Nucleic Acids Res., 2001)

Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins. - Andreas Heger; Liisa Holm (ISMB (Supplement of Bioinformatics), 2003)

Accurate Detection of Very Sparse Sequence Motifs. - Andreas Heger; Michael Lappe; Liisa Holm (J. Comput. Biol., 2004)

POBO, transcription factor binding site verification with bootstrapping. - Matti Kankainen; Liisa Holm (Nucleic Acids Res., 2004)

PSIbase: a database of Protein Structural Interactome map (PSIMAP). - Sungsam Gong; Giseok Yoon; Insoo Jang; Dan M. Bolser; Panos Dafas; Michael Schroeder 001; Hansol Choi; Yoobok Cho; Kyungsook Han; Sunghoon Lee; Hwanho Choi; Michael Lappe; et al. (Bioinform., 2005)

ADDA: a domain database with global coverage of the protein universe. - Andreas Heger; Christopher Andrew Wilton; Ashwin Sivakumar; Liisa Holm (Nucleic Acids Res., 2005)

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. - Matti Kankainen; Liisa Holm (Nucleic Acids Res., 2005)

Bayesian search of functionally divergent protein subgroups and their function specific residues. - Pekka Marttinen; Jukka Corander; Petri Törönen; Liisa Holm (Bioinform., 2006)

POXO: a web-enabled tool series to discover transcription factor binding sites. - Matti Kankainen; Petri Pehkonen; Päivi Rosenström; Petri Törönen; Garry Wong; Liisa Holm (Nucleic Acids Res., 2006)

The global trace graph, a novel paradigm for searching protein sequence databases. - Andreas Heger; Swapan Mallick; Christopher Andrew Wilton; Liisa Holm (Bioinform., 2007)

Searching protein structure databases with DaliLite v.3. - Liisa Holm; S. Kääriäinen; Päivi Rosenström; A. Schenkel (Bioinform., 2008)

PairsDB atlas of protein sequence space. - Andreas Heger; Eija Korpelainen; Taavi Hupponen; Kimmo Mattila; Vesa Ollikainen; Liisa Holm (Nucleic Acids Res., 2008)

Evaluation of Novel Protein Structure Comparison Algorithms Based on Objective Function Rankings. - Hitomi Hasegawa; Liisa Holm (BMEI, 2009)

LOCP - locating pilus operons in Gram-positive bacteria. - Ilya Plyusnin; Liisa Holm; Matti Kankainen (Bioinform., 2009)

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. - Petri Törönen; Pauli J. Ojala; Pekka Marttinen; Liisa Holm (BMC Bioinform., 2009)

Generation of Gene Ontology benchmark datasets with various types of positive signal. - Petri Törönen; Petri Pehkonen; Liisa Holm (BMC Bioinform., 2009)

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels. - Katja Astikainen; Liisa Holm; Esa Pitkänen; Sándor Szedmák; Juho Rousu (BIOSTEC (Selected Papers), 2010)

Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function. - Katja Astikainen; Esa Pitkänen; Juho Rousu; Liisa Holm; Sándor Szedmák (BIOINFORMATICS, 2010)

Inferring the physical connectivity of complex networks from their functional dynamics. - Hung Ta; Chang Yoon; Liisa Holm; Seung Han (BMC Syst. Biol., 2010)

The Pfam protein families database. - Robert D. Finn; Jaina Mistry; John G. Tate; Penny C. Coggill; Andreas Heger; Joanne E. Pollington; O. Luke Gavin; Prasad Gunasekaran; Goran Ceric; Kristoffer Forslund; Liisa Holm; Erik L. L. Sonnhammer; et al. (Nucleic Acids Res., 2010)

Dali server: conservation mapping in 3D. - Liisa Holm; Päivi Rosenström (Nucleic Acids Res., 2010)

MPEA - metabolite pathway enrichment analysis. - Matti Kankainen; Peddinti V. Gopalacharyulu; Liisa Holm; Matej Oresic (Bioinform., 2011)

A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees. - Hung Xuan Ta; Patrik Koskinen; Liisa Holm (Bioinform., 2011)

SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. - Patrik Koskinen; Liisa Holm (Bioinform., 2012)

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. - Matti Kankainen; Teija Ojala; Liisa Holm (BMC Bioinform., 2012)

Comprehensive comparison of graph based multiple protein sequence alignment strategies. - Ilya Plyusnin; Liisa Holm (BMC Bioinform., 2012)

The Pfam protein families database. - Marco Punta; Penny C. Coggill; Ruth Y. Eberhardt; Jaina Mistry; John G. Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; et al. (Nucleic Acids Res., 2012)

GOParGenPy: a high throughput method to generate Gene Ontology data matrices. - Ajay Kumar; Liisa Holm; Petri Törönen (BMC Bioinform., 2013)

Gene set analysis: limitations in popular existing methods and proposed improvements. - Pashupati P. Mishra; Petri Törönen; Yrjö Leino; Liisa Holm (Bioinform., 2014)

Pfam: the protein families database. - Robert D. Finn; Alex Bateman; Jody Clements; Penelope Coggill; Ruth Y. Eberhardt; Sean R. Eddy; Andreas Heger; Kirstie Hetherington; Liisa Holm; Jaina Mistry; Erik L. L. Sonnhammer; John G. Tate; et al. (Nucleic Acids Res., 2014)

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. - Esa Pitkänen; Paula Jouhten; Jian Hou 007; Muhammad Fahad Syed; Peter Blomberg; Jana Kludas; Merja Oja; Liisa Holm; Merja Penttilä; Juho Rousu; Mikko Arvas (PLoS Comput. Biol., 2014)

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment. - Patrik Koskinen; Petri Törönen; Jussi Nokso-Koivisto; Liisa Holm (Bioinform., 2015)

SANSparallel: interactive homology search against Uniprot. - Panu Somervuo; Liisa Holm (Nucleic Acids Res., 2015)

Robust multi-group gene set analysis with few replicates. - Pashupati P. Mishra; Alan Medlar; Liisa Holm; Petri Törönen (BMC Bioinform., 2016)

Dali server update. - Liisa Holm; Laura M. Laakso (Nucleic Acids Res., 2016)

TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases. - Alan Medlar; Liisa Holm (BMC Bioinform., 2018)

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing. - Panu Somervuo; Patrik Koskinen; Peng Mei; Liisa Holm; Petri Auvinen; Lars Paulin (BMC Bioinform., 2018)

Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search. - Reda Younsi; Jing Tang; Liisa Holm (CoRR, 2018)

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. - Alan Medlar; Petri Törönen; Liisa Holm (Nucleic Acids Res., 2018)

PANNZER2: a rapid functional annotation web server. - Petri Törönen; Alan Medlar; Liisa Holm (Nucleic Acids Res., 2018)

Benchmarking fold detection by DaliLite v.5. - Liisa Holm (Bioinform., 2019)

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. - Ilya Plyusnin; Liisa Holm; Petri Törönen (PLoS Comput. Biol., 2019)

A New Approach to Multilabel Stratified Cross Validation with Application to Large and Sparse Gene Ontology Datasets. - Henri Tiittanen; Liisa Holm; Petri Törönen (CoRR, 2021)

Dali server: structural unification of protein families. - Liisa Holm (Nucleic Acids Res., 2022)

Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. - Ilya Plyusnin; Liisa Holm; Petri Törönen (PLoS Comput. Biol., 2022)