Liisa Holm

60 papers A 2B 1Journal 52Unranked 5
YearRankTypeTitle / Venue / Authors
2022 J jnl
Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
PLoS Comput. Biol.
Ilya Plyusnin, Liisa Holm, Petri Törönen
2022 J jnl
Dali server: structural unification of protein families.
Nucleic Acids Res.
Liisa Holm
2021 J jnl
A New Approach to Multilabel Stratified Cross Validation with Application to Large and Sparse Gene Ontology Datasets.
CoRR
Henri Tiittanen, Liisa Holm, Petri Törönen
2019 J jnl
Benchmarking fold detection by DaliLite v.5.
Bioinform.
Liisa Holm
2019 J jnl
Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
PLoS Comput. Biol.
Ilya Plyusnin, Liisa Holm, Petri Törönen
2018 J jnl
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.
Nucleic Acids Res.
Alan Medlar, Petri Törönen, Liisa Holm
2018 J jnl
BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.
BMC Bioinform.
Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen, Lars Paulin
2018 J jnl
PANNZER2: a rapid functional annotation web server.
Nucleic Acids Res.
Petri Törönen, Alan Medlar, Liisa Holm
2018 J jnl
TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases.
BMC Bioinform.
Alan Medlar, Liisa Holm
2018 J jnl
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search.
CoRR
Reda Younsi, Jing Tang, Liisa Holm
2016 J jnl
Dali server update.
Nucleic Acids Res.
Liisa Holm, Laura M. Laakso
2016 J jnl
Robust multi-group gene set analysis with few replicates.
BMC Bioinform.
Pashupati P. Mishra, Alan Medlar, Liisa Holm, Petri Törönen
2015 J jnl
PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.
Bioinform.
Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm
2015 J jnl
SANSparallel: interactive homology search against Uniprot.
Nucleic Acids Res.
Panu Somervuo, Liisa Holm
2014 J jnl
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.
PLoS Comput. Biol.
Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas
2014 J jnl
Gene set analysis: limitations in popular existing methods and proposed improvements.
Bioinform.
Pashupati P. Mishra, Petri Törönen, Yrjö Leino, Liisa Holm
2014 J jnl
Pfam: the protein families database.
Nucleic Acids Res.
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, Marco Punta
2013 J jnl
GOParGenPy: a high throughput method to generate Gene Ontology data matrices.
BMC Bioinform.
Ajay Kumar, Liisa Holm, Petri Törönen
2012 J jnl
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.
BMC Bioinform.
Matti Kankainen, Teija Ojala, Liisa Holm
2012 J jnl
Comprehensive comparison of graph based multiple protein sequence alignment strategies.
BMC Bioinform.
Ilya Plyusnin, Liisa Holm
2012 J jnl
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.
Bioinform.
Patrik Koskinen, Liisa Holm
2012 J jnl
The Pfam protein families database.
Nucleic Acids Res.
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, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn
2011 J jnl
A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees.
Bioinform.
Hung Xuan Ta, Patrik Koskinen, Liisa Holm
2011 J jnl
MPEA - metabolite pathway enrichment analysis.
Bioinform.
Matti Kankainen, Peddinti V. Gopalacharyulu, Liisa Holm, Matej Oresic
2010 J jnl
Dali server: conservation mapping in 3D.
Nucleic Acids Res.
Liisa Holm, Päivi Rosenström
2010 J jnl
Inferring the physical connectivity of complex networks from their functional dynamics.
BMC Syst. Biol.
Hung Ta, Chang Yoon, Liisa Holm, Seung Han
2010 — conf
Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function.
BIOINFORMATICS
Katja Astikainen, Esa Pitkänen, Juho Rousu, Liisa Holm, Sándor Szedmák
2010 — conf
Structured Output Prediction of Novel Enzyme Function with Reaction Kernels.
BIOSTEC (Selected Papers)
Katja Astikainen, Liisa Holm, Esa Pitkänen, Sándor Szedmák, Juho Rousu
2010 J jnl
The Pfam protein families database.
Nucleic Acids Res.
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, Sean R. Eddy, Alex Bateman
2009 — conf
Evaluation of Novel Protein Structure Comparison Algorithms Based on Objective Function Rankings.
BMEI
Hitomi Hasegawa, Liisa Holm
2009 J jnl
Generation of Gene Ontology benchmark datasets with various types of positive signal.
BMC Bioinform.
Petri Törönen, Petri Pehkonen, Liisa Holm
2009 J jnl
LOCP - locating pilus operons in Gram-positive bacteria.
Bioinform.
Ilya Plyusnin, Liisa Holm, Matti Kankainen
2009 J jnl
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.
BMC Bioinform.
Petri Törönen, Pauli J. Ojala, Pekka Marttinen, Liisa Holm
2008 J jnl
PairsDB atlas of protein sequence space.
Nucleic Acids Res.
Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, Liisa Holm
2008 J jnl
Searching protein structure databases with DaliLite v.3.
Bioinform.
Liisa Holm, S. Kääriäinen, Päivi Rosenström, A. Schenkel
2007 J jnl
The global trace graph, a novel paradigm for searching protein sequence databases.
Bioinform.
Andreas Heger, Swapan Mallick, Christopher Andrew Wilton, Liisa Holm
2006 J jnl
Bayesian search of functionally divergent protein subgroups and their function specific residues.
Bioinform.
Pekka Marttinen, Jukka Corander, Petri Törönen, Liisa Holm
2006 J jnl
POXO: a web-enabled tool series to discover transcription factor binding sites.
Nucleic Acids Res.
Matti Kankainen, Petri Pehkonen, Päivi Rosenström, Petri Törönen, Garry Wong, Liisa Holm
2005 J jnl
ADDA: a domain database with global coverage of the protein universe.
Nucleic Acids Res.
Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, Liisa Holm
2005 J jnl
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.
Nucleic Acids Res.
Matti Kankainen, Liisa Holm
2005 J jnl
PSIbase: a database of Protein Structural Interactome map (PSIMAP).
Bioinform.
Sungsam Gong, Giseok Yoon, Insoo Jang, Dan M. Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, Jonghwa Bhak
2004 J jnl
Accurate Detection of Very Sparse Sequence Motifs.
J. Comput. Biol.
Andreas Heger, Michael Lappe, Liisa Holm
2004 J jnl
POBO, transcription factor binding site verification with bootstrapping.
Nucleic Acids Res.
Matti Kankainen, Liisa Holm
2003 B conf
Accurate detection of very sparse sequence motifs.
RECOMB
Andreas Heger, Michael Lappe, Liisa Holm
2003 — conf
Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins.
ISMB (Supplement of Bioinformatics)
Andreas Heger, Liisa Holm
2001 J jnl
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.
Nucleic Acids Res.
Sabine Dietmann, Jong-Chan Park, Cédric Notredame, Andreas Heger, Michael Lappe, Liisa Holm
2001 — conf
Generating protein interaction maps from incomplete data: application to fold assignment.
ISMB (Supplement of Bioinformatics)
Michael Lappe, Jong-Chan Park, Oliver Niggemann, Liisa Holm
2001 J jnl
Picasso: generating a covering set of protein family profiles.
Bioinform.
Andreas Heger, Liisa Holm
2000 J jnl
DaliLite workbench for protein structure comparison.
Bioinform.
Liisa Holm, Jong-Chan Park
2000 J jnl
Estimating the significance of sequence order in protein secondary structure and prediction.
Bioinform.
Jong-Chan Park, Sabine Dietmann, Andreas Heger, Liisa Holm
2000 J jnl
RSDB: representative protein sequence databases have high information content.
Bioinform.
Jong-Chan Park, Liisa Holm, Andreas Heger, Cyrus Chothia
2000 J jnl
Sequence search algorithm assessment and testing toolkit (SAT).
Bioinform.
Jong-Chan Park, Liisa Holm, Cyrus Chothia
1999 J jnl
Protein folds and families: sequence and structure alignments.
Nucleic Acids Res.
Liisa Holm, Chris Sander
1998 J jnl
COFFEE: an objective function for multiple sequence alignments.
Bioinform.
Cédric Notredame, Liisa Holm, Desmond G. Higgins
1998 J jnl
Removing near-neighbour redundancy from large protein sequence collections.
Bioinform.
Liisa Holm, Chris Sander
1998 J jnl
Touring protein fold space with Dali/FSSP.
Nucleic Acids Res.
Liisa Holm, Chris Sander
1997 J jnl
Dali/FSSP classification of three-dimensional protein folds.
Nucleic Acids Res.
Liisa Holm, Chris Sander
1997 A conf
Decision Support System for the Evolutionary Classification of Protein Structures.
ISMB
Liisa Holm, Chris Sander
1996 J jnl
The FSSP database: fold classification based on structure-structure alignment of proteins.
Nucleic Acids Res.
Liisa Holm, Chris Sander
1995 A conf
3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability.
ISMB
Liisa Holm, Chris Sander