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Liisa Holm
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2020 – today
- 2022
- [j50]Liisa Holm
:
Dali server: structural unification of protein families. Nucleic Acids Res. 50(W1): 210-215 (2022) - [j49]Ilya Plyusnin, Liisa Holm, Petri Törönen:
Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. PLoS Comput. Biol. 18(6) (2022) - 2021
- [i2]Henri Tiittanen, Liisa Holm, Petri Törönen:
A New Approach to Multilabel Stratified Cross Validation with Application to Large and Sparse Gene Ontology Datasets. CoRR abs/2109.01425 (2021)
2010 – 2019
- 2019
- [j48]Liisa Holm
Benchmarking fold detection by DaliLite v.5. Bioinform. 35(24): 5326-5327 (2019) - [j47]Ilya Plyusnin
Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. PLoS Comput. Biol. 15(11) (2019) - 2018
- [j46]Panu Somervuo
BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing. BMC Bioinform. 19(1): 257:1-257:6 (2018) - [j45]Alan Medlar, Liisa Holm
TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases. BMC Bioinform. 19(1): 278:1-278:9 (2018) - [j44]Alan Medlar, Petri Törönen
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res. 46(Webserver-Issue): W479-W485 (2018) - [j43]Petri Törönen
PANNZER2: a rapid functional annotation web server. Nucleic Acids Res. 46(Webserver-Issue): W84-W88 (2018) - [i1]Reda Younsi, Jing Tang, Liisa Holm:
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search. CoRR abs/1809.06700 (2018) - 2016
- [j42]Pashupati P. Mishra
Robust multi-group gene set analysis with few replicates. BMC Bioinform. 17: 526:1-526:12 (2016) - [j41]Liisa Holm
Dali server update. Nucleic Acids Res. 44(Webserver-Issue): W351-W355 (2016) - 2015
- [j40]Patrik Koskinen, Petri Törönen
PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment. Bioinform. 31(10): 1544-1552 (2015) - [j39]Panu Somervuo, Liisa Holm
SANSparallel: interactive homology search against Uniprot. Nucleic Acids Res. 43(Webserver-Issue): W24-W29 (2015) - 2014
- [j38]Pashupati P. Mishra
Gene set analysis: limitations in popular existing methods and proposed improvements. Bioinform. 30(19): 2747-2756 (2014) - [j37]Robert D. Finn
Pfam: the protein families database. Nucleic Acids Res. 42(Database-Issue): 222-230 (2014) - [j36]Esa Pitkänen
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. PLoS Comput. Biol. 10(2) (2014) - 2013
- [j35]Ajay Kumar
GOParGenPy: a high throughput method to generate Gene Ontology data matrices. BMC Bioinform. 14: 242 (2013) - 2012
- [j34]Patrik Koskinen, Liisa Holm
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinform. 28(18): 438-443 (2012) - [j33]Matti Kankainen
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. BMC Bioinform. 13: 33 (2012) - [j32]Ilya Plyusnin
Comprehensive comparison of graph based multiple protein sequence alignment strategies. BMC Bioinform. 13: 64 (2012) - [j31]Marco Punta
The Pfam protein families database. Nucleic Acids Res. 40(Database-Issue): 290-301 (2012) - 2011
- [j30]Hung Xuan Ta, Patrik Koskinen, Liisa Holm
A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees. Bioinform. 27(5): 700-706 (2011) - [j29]Matti Kankainen
MPEA - metabolite pathway enrichment analysis. Bioinform. 27(13): 1878-1879 (2011) - 2010
- [j28]Hung Ta
Inferring the physical connectivity of complex networks from their functional dynamics. BMC Syst. Biol. 4: 70 (2010) - [j27]Robert D. Finn
The Pfam protein families database. Nucleic Acids Res. 38(Database-Issue): 211-222 (2010) - [j26]Liisa Holm
Dali server: conservation mapping in 3D. Nucleic Acids Res. 38(Web-Server-Issue): 545-549 (2010) - [c8]Katja Astikainen, Esa Pitkänen, Juho Rousu, Liisa Holm, Sándor Szedmák:
Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function. BIOINFORMATICS 2010: 48-55 - [c7]Katja Astikainen, Liisa Holm
Structured Output Prediction of Novel Enzyme Function with Reaction Kernels. BIOSTEC (Selected Papers) 2010: 367-379
2000 – 2009
- 2009
- [j25]Ilya Plyusnin
LOCP - locating pilus operons in Gram-positive bacteria. Bioinform. 25(9): 1187-1188 (2009) - [j24]Petri Törönen
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinform. 10: 307 (2009) - [j23]Petri Törönen
Generation of Gene Ontology benchmark datasets with various types of positive signal. BMC Bioinform. 10: 319 (2009) - [c6]Hitomi Hasegawa, Liisa Holm
Evaluation of Novel Protein Structure Comparison Algorithms Based on Objective Function Rankings. BMEI 2009: 1-6 - 2008
- [j22]Liisa Holm
Searching protein structure databases with DaliLite v.3. Bioinform. 24(23): 2780-2781 (2008) - [j21]Andreas Heger
PairsDB atlas of protein sequence space. Nucleic Acids Res. 36(Database-Issue): 276-280 (2008) - 2007
- [j20]Andreas Heger
The global trace graph, a novel paradigm for searching protein sequence databases. Bioinform. 23(18): 2361-2367 (2007) - 2006
- [j19]Pekka Marttinen, Jukka Corander, Petri Törönen
Bayesian search of functionally divergent protein subgroups and their function specific residues. Bioinform. 22(20): 2466-2474 (2006) - [j18]Matti Kankainen
POXO: a web-enabled tool series to discover transcription factor binding sites. Nucleic Acids Res. 34(Web-Server-Issue): 534-540 (2006) - 2005
- [j17]Sungsam Gong
PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinform. 21(10): 2541-2543 (2005) - [j16]Andreas Heger
ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res. 33(Database-Issue): 188-191 (2005) - [j15]Matti Kankainen
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. Nucleic Acids Res. 33(Web-Server-Issue): 427-431 (2005) - 2004
- [j14]Andreas Heger
Accurate Detection of Very Sparse Sequence Motifs. J. Comput. Biol. 11(5): 843-857 (2004) - [j13]Matti Kankainen
POBO, transcription factor binding site verification with bootstrapping. Nucleic Acids Res. 32(Web-Server-Issue): 222-229 (2004) - 2003
- [c5]Andreas Heger, Liisa Holm:
Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins. ISMB (Supplement of Bioinformatics) 2003: 130-137 - [c4]Andreas Heger, Michael Lappe, Liisa Holm:
Accurate detection of very sparse sequence motifs. RECOMB 2003: 139-147 - 2001
- [j12]Andreas Heger
Picasso: generating a covering set of protein family profiles. Bioinform. 17(3): 272-279 (2001) - [j11]Sabine Dietmann
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 29(1): 55-57 (2001) - [c3]Michael Lappe, Jong-Chan Park, Oliver Niggemann, Liisa Holm:
Generating protein interaction maps from incomplete data: application to fold assignment. ISMB (Supplement of Bioinformatics) 2001: 149-156 - 2000
- [j10]Jong-Chan Park, Liisa Holm, Cyrus Chothia:
Sequence search algorithm assessment and testing toolkit (SAT). Bioinform. 16(2): 104-110 (2000) - [j9]Jong-Chan Park, Liisa Holm, Andreas Heger
RSDB: representative protein sequence databases have high information content. Bioinform. 16(5): 458-464 (2000) - [j8]Liisa Holm, Jong-Chan Park:
DaliLite workbench for protein structure comparison. Bioinform. 16(6): 566-567 (2000) - [j7]Jong-Chan Park, Sabine Dietmann
Estimating the significance of sequence order in protein secondary structure and prediction. Bioinform. 16(11): 978-987 (2000)
1990 – 1999
- 1999
- [j6]Liisa Holm
Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27(1): 244-247 (1999) - 1998
- [j5]Cédric Notredame, Liisa Holm, Desmond G. Higgins:
COFFEE: an objective function for multiple sequence alignments. Bioinform. 14(5): 407-422 (1998) - [j4]Liisa Holm, Chris Sander:
Removing near-neighbour redundancy from large protein sequence collections. Bioinform. 14(5): 423-429 (1998) - [j3]Liisa Holm
Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26(1): 316-319 (1998) - 1997
- [j2]Liisa Holm
Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res. 25(1): 231-234 (1997) - [c2]Liisa Holm, Chris Sander:
Decision Support System for the Evolutionary Classification of Protein Structures. ISMB 1997: 140-146 - 1996
- [j1]Liisa Holm
The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24(1): 206-209 (1996) - 1995
- [c1]Liisa Holm, Chris Sander:
3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability. ISMB 1995: 179-187
Coauthor Index
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