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  • Finland

  • PL 56 (Viikinkaari 5)

    00014

    Finland

20032021
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Publications 2003 2019

2019

Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search

Younsi, R., Tang, J. & Holm, L. U. T., 29 Jan 2019, (Unpublished) In : arXiv.org .

Research output: Contribution to journalArticleGeneral public

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2018

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

Medlar, A. J., Törönen, P. & Holm, L., 2 Jul 2018, In : Nucleic Acids Research. 46, W1, p. W479-W485 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing

Somervuo, P., Koskinen, P., Mei, P., Holm, L., Auvinen, P. & Paulin, L., 5 Jul 2018, In : BMC Bioinformatics. 19, 257, 6 p., 257.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Bracketing phenogenotypic limits of mammalian hybridization

Savriama, Y., Valtonen, M., Kammonen, J. I., Rastas, P., Smolander, O-P., Lyyski, A., Häkkinen, T. J., Corfe, I. J., Gerber, S., Salazar-Ciudad, I., Paulin, L., Holm, L., Löytynoja, A., Auvinen, P. & Jernvall, J., 28 Nov 2018, In : Royal Society Open Science. 5, 11, 12 p., 180903.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer

Pussila, M., Toronen, P., Einarsdottir, E., Katayama, S., Krjutskov, K., Holm, L., Kere, J., Peltomäki, P., Mäkinen, M. J., Linden, J. & Nyström, M., Jun 2018, In : Carcinogenesis. 39, 6, p. 788-797 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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PANNZER2: a rapid functional annotation web server

Törönen, P., Medlar, A. & Holm, L., 2 Jul 2018, In : Nucleic Acids Research. 46, W1, p. W84-W88 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases

Medlar, A. & Holm, L., 31 Jul 2018, In : BMC Bioinformatics. 19, 9 p., 278.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2017

Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1

Niemi, O., Laine, P., Koskinen, P., Pasanen, M., Pennanen, V., Harjunpaa, H., Nykyri, J., Holm, L., Paulin, L., Auvinen, P., Palva, E. T. & Pirhonen, M., 20 Dec 2017, In : Standards in Genomic Sciences. 12, 8 p., 87.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., Casadio, R. & 127 othersCao, R., Zhong, Z., Cheng, J., Altenhoff, A., Skunca, N., Dessimoz, C., Dogan, T., Hakala, K., Kaewphan, S., Mehryary, F., Salakoski, T., Ginter, F., Fang, H., Smithers, B., Oates, M., Gough, J., Toronen, P., Koskinen, P., Holm, L., Chen, C-T., Hsu, W-L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., Dukka, B. K. C., Khan, I. K., Kihara, D., Ofer, D., Rappoport, N., Stern, A., Cibrian-Uhalte, E., Denny, P., Foulger, R. E., Hieta, R., Legge, D., Lovering, R. C., Magrane, M., Melidoni, A. N., Mutowo-Meullenet, P., Pichler, K., Shypitsyna, A., Li, B., Zakeri, P., ElShal, S., Tranchevent, L-C., Das, S., Dawson, N. L., Lee, D., Lees, J. G., Sillitoe, I., Bhat, P., Nepusz, T., Romero, A. E., Sasidharan, R., Yang, H., Paccanaro, A., Gillis, J., Sedeno-Cortes, A. E., Pavlidis, P., Feng, S., Cejuela, J. M., Goldberg, T., Hamp, T., Richter, L., Salamov, A., Gabaldon, T., Marcet-Houben, M., Supek, F., Gong, Q., Ning, W., Zhou, Y., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Toppo, S., Ferrari, C., Giollo, M., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernandez, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A. D. J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., 7 Sep 2016, In : Genome Biology. 17, 19 p., 184.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Dali server update

Holm, L. & Laakso, L. M., 8 Jul 2016, In : Nucleic Acids Research. 44, W1, p. W351-W355 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Robust multi-group gene set analysis with few replicates

Mishra, P. P., Medlar, A., Holm, L. & Törönen, P., 9 Dec 2016, In : BMC Bioinformatics. 17, 12 p., 526.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Flight-induced changes in gene expression in the Glanville fritillary butterfly

Kvist, J., Mattila, A. L. K., Somervuo, P., Ahola, V., Koskinen, P., Paulin, L., Salmela, L., Fountain, T., Rastas, P., Ruokolainen, A., Taipale, M., Holm, L., Auvinen, P., Lehtonen, R., Frilander, M. J. & Hanski, I., Oct 2015, In : Molecular Ecology. 24, 19, p. 4886-4900 15 p.

Research output: Contribution to journalArticleScientificpeer-review

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment

Koskinen, P., Törönen, P., Nokso-Koivisto, J. & Holm, L., 2015, In : Bioinformatics. 31, 10, p. 1544-1552 9 p.

Research output: Contribution to journalArticleScientificpeer-review

SANSparallel: interactive homology search against Uniprot

Somervuo, P. & Holm, L., 1 Jul 2015, In : Nucleic Acids Research. 43, W1, p. W24-W29 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2014

Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes

Wang, H., Fewer, D. P., Holm, L., Rouhiainen, L. & Sivonen, K., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 25, p. 9259-9264 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. & Arvas, M., Feb 2014, In : PLoS Computational Biology. 10, 2, p. e1003465 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis

Ojala, T., Kankainen, M., Castro, J., Cerca, N., Edelman, S., Westerlund-Wikstroem, B., Paulin, L., Holm, L. & Auvinen, P., 5 Dec 2014, In : BMC Genomics. 15, 21 p., 1070.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Gene set analysis: limitations in popular existing methods and proposed improvements

Mishra, P., Törönen, P., Leino, Y. & Holm, L., 2014, In : Bioinformatics. 30, 19, p. 2747-2756 10 p., btu374.

Research output: Contribution to journalArticleScientificpeer-review

Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains

Savijoki, K., Iivanainen, A., Siljamaki, P., Laine, P. K., Paulin, L., Karonen (os. Miettinen), T., Pyörälä, S., Kankainen, M., Nyman, T. A., Salomaki, T., Koskinen, P., Holm, L., Simojoki, H., Taponen, S., Sukura, A., Kalkkinen, N., Auvinen, P. & Varmanen, P., Aug 2014, In : Journal of Proteome Research. 13, 8, p. 3748-3762 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Pfam: the protein families database

Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., Sonnhammer, E. L. L., Tate, J. & Punta, M., 2014, In : Nucleic Acids Research. 42, D1, p. D222-D230 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Valimaki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E. A., Ferguson, L. C., Luo, S., Cao, Z., de Jong, M. A., Duplouy, A., Smolander, O-P., Vogel, H., McCoy, R. C. & 27 othersQian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J. K., Joshi, A., Salojarvi, J., Wheat, C. W., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkanen, E., Ylinen, J., Waterhouse, R. M., Turunen, M., Vaharautio, A., Ojanen, S. P., Schulman, A. H., Taipale, M., Lawson, D., Ukkonen, E., Makinen, V., Goldsmith, M. R., Holm, L., Auvinen, P., Frilander, M. J. & Hanski, I., Sep 2014, In : Nature Communications. 5, 9 p., 4737.

Research output: Contribution to journalArticleScientificpeer-review

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

Somervuo, P., Kvist, J., Ikonen, S., Auvinen, P., Paulin, L., Koskinen, P., Holm, L., Taipale, M., Duplouy, A., Ruokolainen, A., Saarnio, S., Siren, J., Kohonen, J., Corander, J., Frilander, M. J., Ahola, V. & Hanski, I., 2 Jul 2014, In : PLoS One. 9, 7, 12 p., 101467.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2013

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., Pandey, G., Yunes, J. M., Talwalkar, A. S., Repo, S., Souza, M. L., Piovesan, D., Casadio, R., Wang, Z., Cheng, J., Fang, H. & 82 othersGoughl, J., Koskinen, P., Toronen, P., Nokso-Koivisto, J., Holm, L., Cozzetto, D., Buchan, D. W. A., Bryson, K., Jones, D. T., Limaye, B., Inamdar, H., Datta, A., Manjari, S. K., Joshi, R., Chitale, M., Kihara, D., Lisewski, A. M., Erdin, S., Venner, E., Lichtarge, O., Rentzsch, R., Yang, H., Romero, A. E., Bhat, P., Paccanaro, A., Hamp, T., Kassner, R., Seemayer, S., Vicedo, E., Schaefer, C., Achten, D., Auer, F., Boehm, A., Braun, T., Hecht, M., Heron, M., Hoenigschmid, P., Hopf, T. A., Kaufmann, S., Kiening, M., Krompass, D., Landerer, C., Mahlich, Y., Roos, M., Bjorne, J., Salakoski, T., Wong, A., Shatkay, H., Gatzmann, F., Sommer, I., Wass, M. N., Sternberg, M. J. E., Skunca, N., Supek, F., Bosnjak, M., Panov, P., Dzeroski, S., Smuc, T., Kourmpetis, Y. A. I., van Dijk, A. D. J., ter Braak, C. J. F., Zhou, Y., Gong, Q., Dong, X., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Di Camillo, B., Toppo, S., Lan, L., Djuric, N., Guo, Y., Vucetic, S., Bairoch, A., Linial, M., Babbitt, P. C., Brenner, S. E., Orengo, C., Rost, B., Mooney, S. D. & Friedberg, I., Mar 2013, In : Nature methods. 10, 3, p. 221-227 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Automated sequence-based approaches for identifying domain families

Holm, L. & Heger, A., 2013, Protein Families: Relating Protein Sequence, Structure, and Function. John Wiley & Sons Ltd. , p. 1-24 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientific

Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis

Li, J., Besseau, S., Törönen, P., Sipari, N. H., Kollist, H., Holm, L. & Palva, E. T., Oct 2013, In : New Phytologist. 200, 2, p. 457–472 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase Clusters

Garlant, L., Koskinen, P., Rouhiainen, L. A. O., Laine, P., Paulin, L., Auvinen, P., Holm, L. & Pirhonen, M., 2013, In : Diversity. 5, 4, p. 824-842 19 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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GOParGenPy: a high throughput method to generate Gene Ontology data matrices

Kumar, A. A., Holm, L. & Toronen, P., 8 Aug 2013, In : BMC Bioinformatics. 14, 242, 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2012

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

Kankainen, M., Ojala, T. & Holm, L., 2012, In : BMC Bioinformatics. 13, 33, p. Article Number: 33 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Comprehensive comparison of graph based multiple protein sequence alignment strategies

Plyusnin, I. & Holm, L., 29 Apr 2012, In : BMC Bioinformatics. 13, p. 64 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Genome Sequence of Pectobacterium sp. Strain SCC3193

Koskinen, J. P., Laine, P., Niemi, O., Nykyri, J., Harjunpää, H., Auvinen, P., Paulin, L., Pirhonen, M., Palva, T. & Holm, L., Nov 2012, In : Journal of Bacteriology. 194, 21, p. 6004 1 p.

Research output: Contribution to journalArticleScientificpeer-review

Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients.

Kantelinen, J., Kansikas, M., Candelin, S., Hampel, H., Smith, B., Holm, L., Kariola, R. & Nyström, M., 2012, In : Human Mutation. 33, 8, p. 1294-1301 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Mutational analysis of positively charged amino acid residues of Uukuniemi phlebovirus nucleocapsid protein

Katz, A., Freiberg, A. N., Backstrom, V., Holm, L., Vaheri, A., Flick, R. & Plyusnin, A., 2012, In : Virus Research. 167, 1, p. 118-123 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193

Nykyri, J., Niemi, O. A., Koskinen, P., Nokso-Koivisto, J. P., Pasanen, M., Broberg, E. M., Plyusnin, I., Törönen, P., Holm, L., Pirhonen, M. & Palva, E. T., 2012, In : PLoS Pathogens. 8, 11 (e1003013), 18 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Koskinen, J. P. & Holm, L., 15 Sep 2012, In : Bioinformatics. 28, 18, p. i438-i443 6 p.

Research output: Contribution to journalArticleScientificpeer-review

The Pfam protein families database

Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E. L. L., Eddy, S. R., Bateman, A. & Finn, R. D., Jan 2012, In : Nucleic Acids Research. 40, D1, p. D290-D301 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2011

Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli

Kylväjä, R., Kankainen, M., Holm, L. & Westerlund-Wikström, B., May 2011, In : BMC Microbiology. 11, 117, p. 1-13 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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A Novel Method for Assigning Functional Linkages to Proteins Using Enhanced Phylogenetic Trees

Ta, X. H., Koskinen, P. & Holm, L., 2011, In : Bioinformatics. 27, 5, p. 700-706 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Immunological Effects of Low-dose Cyclophosphamide in Cancer Patients Treated With Oncolytic Adenovirus

Cerullo, V., Diaconu, I., Kangasniemi, L., Rajecki, M., Escutenaire, S., Koski, A., Romano, V., Rouvinen, N., Tuuminen, T., Laasonen, L., Partanen, K., Kauppinen, S., Joensuu, T., Oksanen, M., Holm, S-L., Haavisto, E., Karioja-Kallio, A., Kanerva, A., Pesonen, S., Arstila, P. T. & 1 othersHemminki, A., 2011, In : Molecular therapy. 19, 9, p. 1737-1746 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

In vivo and in vitro distribution of type 5 and fiber-modified oncolytic adenoviruses in human blood compartments

Escutenaire, S., Cerullo, V., Diaconu, I., Ahtiainen, L., Hannuksela, P., Oksanen, M., Haavisto, E., Karioja-Kallio, A., Holm, S-L., Kangasniemi, L., Ribacka, C., Kauppinen, S., Joensuu, T. K., Arstila, T. P., Pesonen, S., Kanerva, A. & Hemminki, A., 2011, In : Annals of Medicine. 43, 2, p. 151-163 13 p.

Research output: Contribution to journalArticleScientificpeer-review

MPEA-metabolite pathway enrichment analysis

Kankainen, M., Gopalacharyulu, P., Holm, L. & Oresic, M., 2011, In : Bioinformatics Trends. 27, 13, p. 1878-1879 2 p.

Research output: Contribution to journalArticleScientificpeer-review

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

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

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
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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