Publications 2003 2019

2011

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels

Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J., 28 Feb 2011, Biomedical Engineering Systems and Technologies: Third International Joint Conference, BIOSTEC 2010, Valencia, Spain, January 20-23, 2010, Revised Selected Papers. Fred, A., Filipe, J. & Gamboa, H. (eds.). Springer, p. 367-379 13 p. (Communications of Computer and Information Science; vol. 127).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2010

A Randomized Sphere Cover Classifier

Younsi, R. & Bagnall, A., 2010, INTELLIGENT DATA ENGINEERING AND AUTOMATED LEARNING - IDEAL 2010. Fyfe, C., Tino, P., Charles, D., GarciaOsorio, C. & Yin, HJ. (eds.). Springer-Verlag, p. 234-241 8 p. (Lecture Notes in Computer Science; vol. 6283).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Dali server: conservation mapping in 3D

Holm, L. & Rosenström, P., 2010, In : Nucleic Acids Research. 38, supplement 2, p. W545-W549 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Genome Sequence of Lactobacillus crispatus ST1

Ojala, T., Kuparinen, V., Koskinen, P., Alatalo, R. M. E., Holm, L., Auvinen, P., Edelman, S., Westerlund-Wikström, B., Korhonen, T., Paulin, L. G. & Kankainen, M., 2010, In : Journal of Bacteriology. 192, 13, p. 3547-3548 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions

Pehkonen, P., Wong, G. & Törönen, P., 2010, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7, 1, p. 37-49 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Inferring the physical connectivity of complex networks from their functional dynamics

Ta, H. X., Yoon, C. N., Holm, L. & Han, S. K., 2010, In : BMC Systems Biology. 4, 12 p., 70.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Oligomerization of Uukuniemi virus nucleocapsid protein

Katz, A., Freiberg, A. N., Backstrom, V., Schulz, A. R., Mateos, A., Holm, L., Pettersson, R. F., Vaheri, A., Flick, R. & Plyusnin, A., 2010, In : Virology Journal. 7, 13 p., 187.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Reaction Kernels: Structured Output Prediction Approaches for Novel Enzyme Function

Astikainen, K., Pitkänen, E., Rousu, J., Holm, L. & Szedmak, S., 20 Jan 2010, Proceedings of the First International Conference on Bioinformatics. Fred, A., Filipe, J. & Gamboa, H. (eds.). The Institute for Systems and Technologies of Information, Control and Communication, p. 48-55

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

The Pfam protein families database

Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E. L. L., Eddy, S. R. & Bateman, A., 2010, In : Nucleic Acids Research. 38, p. D211-D222 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2009

Advances and pitfalls of protein structural alignment

Hasegawa, H. & Holm, L. U. T., 2009, In : Current Opinion in Structural Biology. 19, p. 341-348 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Evaluation of different domain-based methods in protein interaction prediction

Ta, X. H. & Holm, L., 2009, In : Biochemical and Biophysical Research Communications. 390, 3, p. 357-362 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Evaluation of Novel Protein Structure Comparison Algorithms based on Objective Function Rankings

Hasegawa, H. & Holm, L., 2009, Biomedical Engineering and Informatics, 2009. BMEI '09. 2nd International Conference on. Tianjin, p. 1438-1443 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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

Törönen, P., Pehkonen, P. & Holm, L. U. T., 2009, In : BMC Bioinformatics. 10, 319, 14 s

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Interspliced transcription chimeras: neglected pathological mechanism infiltrating gene accession queries?

Tolvanen, M., Ojala, P. J., Törönen, P., Anderson, H., Partanen, J. & Turpeinen, H., 2009, In : Journal of Biomedical Informatics. 42, p. 382-389 8 p.

Research output: Contribution to journalArticleScientificpeer-review

LOCP - locating pilus operons in Gram-positive bacteria

Plyusnin, I., Holm, L. & Kankainen, M., 2009, In : Bioinformatics. 25, 9, p. 1187-1188 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Reaction kernels: predicting enzyme functions you have never seen before

Astikainen, K., Holm, L. U. T., Pitkänen, E. & Rousu, J., 2009, Helsinki: Helsingin yliopisto, tietojenkäsittelytieteen laitos. 13 p.

Research output: Book/ReportBookScientificpeer-review

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

Törönen, P., Ojala, P. J., Marttinen, P. & Holm, L. U. T., 2009, In : BMC Bioinformatics. 10, p. 307

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2008

PairsDB atlas of protein sequence space

Heger, A., Korpelainen, E., Hupponen, T., Mattila, K., Ollikainen, V. & Holm, L., 2008, In : Nucleic Acids Research. 36, p. D276-D280 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Searching protein structure databases with DaliLite v.3

Holm, L., Kääriäinen, S., Rosenström, P. & Schenkel, A., 2008, In : Bioinformatics. 24, 23, p. 2780-2781 2 p.

Research output: Contribution to journalArticleScientificpeer-review

2007

Loss of neurturin in frog: comparative genomics study of GDNF family ligand-receptor pairs

Hätinen, T., Holm, L. & Airaksinen, M. S., 2007, In : Molecular and Cellular Neuroscience. 34, 2, p. 155-167 13 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Heger, A., Mallick, S., Wilton, C. & Holm, L., 2007, In : Bioinformatics. 23, 18, p. 2361-2367 7 p.

Research output: Contribution to journalArticleScientificpeer-review

The RPSP: Web server for prediction of signal peptides

Plewczynski, D., Slabinski, L., Tkacz, A., Kajan, L., Holm, L., Ginalski, K. & Rychlewski, L., 2007, In : Polymer. 48, 19, p. 5493-5496 4 p.

Research output: Contribution to journalArticleScientificpeer-review

Towards structured output prediction of enzyme function (extended abstract)

Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J., 2007, Proceedings of the International Workshop on Machine Learning in Systems Biology 2007, MLSB'07, September 24-25, 2007, Evry, France: Universite d'Evry-Val d'Essonne 2007. p. 27-32 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Transcriptome teleonomy and scavenger lipidomics of albumin and alpha 1-acid glycoproteins: contextual genome-wide ontology enrichment as evidence for the epigenetic code?

Ojala, P., Kilpinen, S., Arola, L., Toronen, P., Bucher, E., Ojala, K., Iljin, K., Peltonen, M., Skotheim, R., Kleivi, K., Tolvanen, M., Autio, R., Somerharju, P., Kallioniemi, O. & Laitinen, S., Sep 2007, In : Chemistry and Physics of Lipids. 149, p. S86-S86 1 p.

Research output: Contribution to journalArticleScientificpeer-review

2006

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

Marttinen, P., Corander, J., Törönen, P. & Holm, L., 2006, In : Bioinformatics. 22, 20, p. 2466-2474 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Evolution and the GDNF family ligands and receptors

Airaksinen, M. S., Holm, L. & Hätinen, T., 2006, In : Brain, Behavior and Evolution. 68, 3, p. 181-190 10 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

From sequences to a functional unit

Sivakumar, A., Wilton, C. & Holm, L., 2006, In : Physiological Genomics. 25, p. 1-8 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Oligomerization of hantavirus nucleocapsid protein: analysis of the N-terminal coiled-coil domain

Alminaite, A., Halttunen, V., Kumar, V., Vaheri, A., Holm, L. & Plyusnin, A., 2006, In : Journal of Virology. 80, 18, p. 9073-9081 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Kankainen, M., Pehkonen, P., Rosenström, P., Törönen, P., Wong, G. & Holm, L., 2006, In : Nucleic Acids Research. 34, p. W534-W540

Research output: Contribution to journalArticleScientificpeer-review

2005

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

Heger, A., Wilton, C. A., Sivakumar, A. & Holm, L., 2005, In : Nucleic Acids Research. 33, p. D188-D191

Research output: Contribution to journalArticleScientificpeer-review

Algorithms for protein interaction networks

Lappe, M. & Holm, L., 2005, In : Biochemical Society Transactions. 33, 3, p. 530-534 5 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Kankainen, M. & Holm, L., 2005, In : Nucleic Acids Research. 33, p. W427-W431

Research output: Contribution to journalArticleScientificpeer-review

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

Gong, S., Yoon, G., Jang, I., Bolser, D., Dafas, P., Schroeder, M., Choi, H., Cho, Y., Han, K., Lee, S., Choi, H., Lappe, M., Holm, L., Kim, S., Oh, D. & Bhak, J., 2005, In : Bioinformatics. 21, 10, p. 2541-2543 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Theme discovery from gene lists for identification and viewing of multiple functional groups

Pehkonen, P., Wong, G. & Törönen, P., 2005, In : BMC Bioinformatics. 6, 162, 18 s

Research output: Contribution to journalArticleScientificpeer-review

2004

Accurate detection of very sparse sequence motifs

Heger, A., Lappe, M. & Holm, L., 2004, In : Journal of Computational Biology. 11, p. 843-857 15 p.

Research output: Contribution to journalArticleScientificpeer-review

POBO, transcription factor binding site verification with bootstrapping

Kankainen, M. & Holm, L., 1 Jul 2004, In : Nucleic Acids Research. 32, p. W222-W229 8 p.

Research output: Contribution to journalArticleScientificpeer-review

2003

Exhaustive enumeration of protein domain families

Heger, A. & Holm, L., 2003, In : Journal of Molecular Biology. 328, p. 749-767 19 p.

Research output: Contribution to journalArticleScientificpeer-review