Group Publications

2012

J Nykyri, O Niemi, P Koskinen, J Nokso-Koivisto, M Pasanen, M Broberg, I ... Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193 PLoS Pathogens 8 (11), e1003013 1 2012

JP Koskinen, P Laine, O Niemi, J Nykyri, H Harjunpää, P Auvinen, L Paulin, M ... Genome Sequence of Pectobacterium sp. Strain SCC3193 Journal of bacteriology 194 (21), 6004-6004 2012

JP Koskinen, L Holm SANS: high-throughput retrieval of protein sequences allowing 50% mismatches Bioinformatics 28 (18), i438-i443 1 2012

J Kantelinen, M Kansikas, S Candelin, H Hampel, B Smith, L Holm, R Kariola ... Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients Human Mutation 2012

I Plyusnin, L Holm Comprehensive comparison of graph based multiple protein sequence alignment strategies BMC bioinformatics 13 (1), 64 3 2012

A Katz, AN Freiberg, V Backström, L Holm, A Vaheri, R Flick, A Plyusnin Mutational analysis of positively charged amino acid residues of Uukuniemi phlebovirus nucleocapsid protein Virus Research

Tollenaere, CMJ, Susi, H, Nokso-Koivisto, JP, Koskinen, P, Tack, AJM, Auvinen, P, Paulin, L, Frilander, M, Lehtonen, RJ, Laine, A-L 2012, 'SNP Design from 454 Sequencing of Podosphaera plantaginis Transcriptome Reveals a Genetically Diverse Pathogen Metapopulation with High Levels of Mixed-Genotype Infection' PLoS One, vol 7, no. 12, pp. e52492.

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD. The Pfam protein families database.

Kankainen M, Ojala TA, Holm L. BLANNOTATOR: enhanced homology-based function prediction of bacterialproteins

2011

Astikainen K, Holm L, Pitkänen E, Szedmak S, Rousu J (2011) Structured output prediction of novel enzyme function with reaction kernels. Biomedical Engineering Systems and Technologies: Communications in Computer and Information Science, 127. Springer Verlag

Won Sup Kim, Xue-Mei Cui, Chang No Yoon, Hung Xuan Ta and Seung Kee Han. Estimating network link weights from inverse phase synchronization indices.

Kylväjä R, Kankainen M, Holm L, Westerlund-Wikström B. Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli.

Ta XH, Koskinen P and Holm L. A Novel Method for Assigning Functional Linkages to Proteins Using Enhanced Phylogenetic Trees.

Kankainen M, Gopalacharyulu P, Holm L and Ore¨i? M. MPEA - metabolite pathway enrichment analysis.

2010

Holm Liisa, Rosenström Päivi. Dali server: conservation mapping in 3D.

Ta XH, Holm L, Yoon CN, Han SK. Inferring the physical connectivity of complex networks from their functional dynamics.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database.

Pehkonen P, Wong G, Törönen P. Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions

2009

H.X. Ta, L. Holm, Evaluation of different domain-based methods in protein interaction prediction.

Koskenniemi K, Koponen J, Kankainen M, Savijoki K, Tynkkynen S, de Vos WM, Kalkkinen N, Varmanen P. Proteome analysis of Lactobacillus rhamnosus GG using 2-D DIGE and mass spectrometry shows differential protein production in laboratory and industrial-type growth media.

Kankainen et al. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein

Petri Törönen, Petri Pehkonen and Liisa Holm. Generation of Gene Ontology benchmark datasets with various types of positive signal

Petri Toronen, Pauli J Ojala, Pekka Marttinen and Liisa Holm. Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.

Tolvanen M, Ojala PJ, Törönen P, Anderson H, Partanen J, Turpeinen H. Interspliced transcription chimeras: Neglected pathological mechanism infiltrating gene accession queries?

Hasegawa Hitomi, Holm Liisa. Advances and pitfalls of protein structural alignment

Plyusnin I, Holm L, Kankainen M. LOCP--locating pilus operons in gram-positive bacteria.

2008

Salusjärvi L, Kankainen M, Soliymani R, Pitkänen JP, Penttilä M, Ruohonen L. Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae.

Astikainen K, Holm L, Pitkänen E, Szedmak S, Rousu J. Towards structured output prediction of enzyme function.

Martti Tolvanen, Pauli J. Ojala, Petri Törönen, Heidi Anderson, Jukka Partanen and Hannu Turpeinen. Interspliced transcription chimeras: Pathological mechanism infiltrating gene accession queries?

Pehkonen, Wong, Toronen. Heuristic Bayesian segmentation for discovery of co-expressed genes within genomic regions

Holm L, Kääriäinen S, Rosenström P, Schenkel A. Searching protein structure databases with DaliLite v.3.

Heger A, Korpelainen E, Hupponen T, Mattila K, Ollikainen V, Holm L. PairsDB atlas of protein sequence space.

2007

Heger A, Mallick S, Wilton C, Holm L. The global trace graph, a novel paradigm for searching protein sequence databases

Pauli Ojala,Sami Kilpinen, Lotta Arola, Petri Törönen, Elmar Bucher, Kalle Ojala, Kristiina Iljin, Mari Peltonen, Rolf Skotheim, Kristine Kleivi, Martti Tolvanen, Reija Autio, Pentti Somerharju, Olli Kallioniemi and Saara Laitinen. Transcriptome teleonomy and scavenger lipidomics of albumin and alpha 1-acid glycoproteins: contextual genome-wide ontology enrichment as evidence for the epigenetic code?

Kankainen M, Löytynoja A. MATLIGN: a motif clustering, comparison and matching tool

Hatinen T, Holm L, Airaksinen M. Loss of neurturin in frog - Comparative genomics study of GDNF family ligand-receptor pairs.

2006

Marttinen P, Corander J, Toronen P, Holm L. Bayesian search of functionally divergent protein subgroups and their function specific residues.

Alminaite A, Halttunen V, Kumar V, Vaheri A, Holm L, Plyusnin A. Oligomerization of hantavirus nucleocapsid protein: analysis of the N-terminal coiled-coil domain.

Hintsanen P, Sevon P, Onkamo P, Eronen L, Toivonen H. An empirical comparison of case-control and trio based study designs in high throughput association mapping.

Kankainen M, Pehkonen P, Rosenstom P, Toronen P, Wong G, Holm L. POXO: a web-enabled tool series to discover transcription factor binding sites.

Airaksinen MS, Holm L, Hatinen T. Evolution of the GDNF family ligands and receptors.

Kankainen M, Brader G, Toronen P, Palva ET, Holm L. Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.

Onkamo P, Toivonen H. A survey of data mining methods for linkage disequilibrium mapping. (Review)

Sivakumar A, Wilton C, Holm L. From sequences to a functional unit.

Sillen A, Forsell C, Lilius L, Axelman K, Bjork BF, Onkamo P, Kere J, Winblad B, Graff C. Genome scan on Swedish Alzheimer's disease families.

Holm L, Kääriäinen S, Plewczynski D, Wilton C. Using Dali for Structural Comparison of Proteins. Current Protocols in Bioinformatics (Wiley publishing).

2005

Pehkonen P, Wong G, Toronen P. Theme discovery from gene lists for identification and viewing of multiple functional groups.

Kankainen M, Holm L. POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.

Lappe M, Holm L. Algorithms for protein interaction networks.

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

Heger A, Wilton C, Sivakumar A, Holm L. ADDA: a domain database with global coverage of the protein universe.

2004

Lappe M, Holm L. Unravelling protein interaction networks with near-optimal efficiency.

Kankainen M, Holm L. POBO, transcription factor binding site verification with bootstrapping.

2003

Heger A, Holm L. More for less in structural genomics.

Matthieu Louis. A theoretical model for the regulation of Sex-lethal gene, Ph.D. thesis, University of Cambridge.

Louis M, Liisa Holm, Sanchez L, Kaufman M. A theoretical Model for the regulation of Sex-lethal, a gene that controls sex determination and dosage compensation in Drosophila melanogaster.

Andreas Heger, Liisa Holm. Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins.

Andreas Heger, Michael Lappe, Liisa Holm. Accurate detection of very sparse sequence motifs.

Heger A, Holm L. Exhaustive enumeration of protein domain families.

2002

Dietmann S, Fernandez-Fuentes N, Holm L. Automated detection of remote homology.

2001

Dietmann S, Holm L. Identification of homology in protein structure classification.

Lappe M, Park J, Niggemann O, Holm L. Generating protein interaction maps from incomplete data: application to fold assignment.

Heger A, Holm L. Picasso: generating a covering set of protein family profiles.

Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.

2000

Park J, Dietmann S, Heger A, Holm L. Estimating the significance of sequence order in protein secondary structure and prediction.

Heger A, Holm L. Towards a covering set of protein family profiles.

Holm L, Park J. DaliLite workbench for protein structure comparison.

Heger A, Holm L. Rapid automatic detection and alignment of repeats in protein sequences.

Park J, Holm L, Heger A, Chothia C. RSDB: representative protein sequence databases have high information content.

Park J, Holm L, Chothia C. Sequence search algorithm assessment and testing toolkit (SAT).

1999

Holm L, Sander C. Protein folds and families: sequence and structure alignments.

1998

Holm L, Unification of protein families.

Notredame C, Holm L, Higgins DG. COFFEE: an objective function for multiple sequence alignments.

Holm L, Sander C. Dictionary of recurrent domains in protein structures.

Holm L, Sander C. Removing near-neighbour redundancy from large protein sequence collections.

Holm L, Sander C. Touring protein fold space with Dali/FSSP.

1997

Karplus K, Sjolander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C. Predicting protein structure using hidden Markov models.

Holm L, Sander C. Decision support system for the evolutionary classification of protein structures.

Holm L, Sander C. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease.

Holm L, Sander C. Enzyme HIT.

Holm L, Sander C. New structure - novel fold?

Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds.

1996

Holm L, Sander C. Mapping the protein universe.

Holm L, Sander C. Alignment of three-dimensional protein structures: network server for database searching.

Holm L, Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins.

1995

Holm L, Sander C. Dali: a network tool for protein structure comparison.

Holm L, Sander C. DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily.

Bork P, Holm L, Koonin EV, Sander C. The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction.

Holm L, Sander C. Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme.

Holm L, Sander C. 3-D lookup: fast protein structure database searches at 90% reliability.

1994

Holm L, Sander C, Ruterjans H, Schnarr M, Fogh R, Boelens R, Kaptein R. LexA repressor and iron uptake regulator from Escherichia coli: new members of the CAP-like DNA binding domain superfamily.

Bork P, Holm L, Sander C. The immunoglobulin fold. Structural classification, sequence patterns and common core.

Holm L, Sander C. The FSSP database of structurally aligned protein fold families.

Holm L, Sander C. Parser for protein folding units.

Holm L, Sander C. Searching protein structure databases has come of age.

Holm L, Sander C, Murzin A. Three sisters, different names.

Holm L, Sander C. Structural similarity of plant chitinase and lysozymes from animals and phage. An evolutionary connection.

1993

Holm L, Sander C. Protein structure comparison by alignment of distance matrices.

Holm L, Sander C. Globin fold in a bacterial toxin.

Holm L, Sander C. Structural alignment of globins, phycocyanins and colicin A.

1992

Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G. A database of protein structure families with common folding motifs.

Holm L, Sander C. Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology.

Holm L, Sander C. Evaluation of protein models by atomic solvation preference.

1991

Holm L, Sander C. Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.