Publications 2003 2019

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Younsi, R., Tang, J. & Holm, L. U. T., 29 Jan 2019, (Unpublished) In : arXiv.org .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

File
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
File

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
File

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
File

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
File

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
File
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
File

HaploForge: a comprehensive pedigree drawing and haplotype visualization web application

Tekman, M., Medlar, A., Mozere, M., Kleta, R. & Stanescu, H., 15 Dec 2017, In : Bioinformatics. 33, 24, p. 3871-3877 7 p.

Research output: Contribution to journalArticleScientificpeer-review

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
File

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
File

Ensembles of random sphere cover classifiers

Younsi, R. & Bagnall, A., Jan 2016, In : Pattern Recognition. 49, p. 213-225 13 p.

Research output: Contribution to journalArticleScientificpeer-review

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
File

Wasabi: an integrated platform for evolutionary sequence analysis and data visualization

Veidenberg, A., Medlar, A. & Löytynoja, A., Apr 2016, In : Molecular Biology and Evolution. 33, 4, p. 1126-1130 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

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
File
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
File

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
File

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
File

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
File
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

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
File

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
File

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
File
2012

An efficient randomised sphere cover classifier

Younsi, R., 1 Jan 2012, In : International Journal of Data Mining, Modelling and Management (IJDMMM). 4, 2, p. 156 171 p.

Research output: Contribution to journalArticleScientificpeer-review

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
File

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
File

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
File
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
File

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

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
File

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
File

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