Patrik Koskinen
Patrik Koskinen
HUS - Helsinki University Hospital
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A large-scale evaluation of computational protein function prediction
P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ...
Nature methods 10 (3), 221-227, 2013
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ...
Genome biology 17, 1-19, 2016
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
V Ahola, R Lehtonen, P Somervuo, L Salmela, P Koskinen, P Rastas, ...
Nature communications 5 (1), 4737, 2014
Cytokinin and auxin display distinct but interconnected distribution and signaling profiles to stimulate cambial activity
J Immanen, K Nieminen, OP Smolander, M Kojima, JA Serra, P Koskinen, ...
Current Biology 26 (15), 1990-1997, 2016
PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment
P Koskinen, P Törönen, J Nokso-Koivisto, L Holm
Bioinformatics 31 (10), 1544-1552, 2015
Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193
J Nykyri, O Niemi, P Koskinen, J Nokso-Koivisto, M Pasanen, M Broberg, ...
PLoS Pathogens 8 (11), e1003013, 2012
SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed-genotype infection
C Tollenaere, H Susi, J Nokso-Koivisto, P Koskinen, A Tack, P Auvinen, ...
PLoS One 7 (12), e52492, 2012
Genome sequence of Lactobacillus crispatus ST1
T Ojala, V Kuparinen, JP Koskinen, E Alatalo, L Holm, P Auvinen, ...
Journal of Bacteriology 192 (13), 3547-3548, 2010
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 …
L Garlant, P Koskinen, L Rouhiainen, P Laine, L Paulin, P Auvinen, ...
Diversity 5 (4), 824-842, 2013
BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing
P Somervuo, P Koskinen, P Mei, L Holm, P Auvinen, L Paulin
BMC bioinformatics 19, 1-6, 2018
Flight‐induced changes in gene expression in the Glanville fritillary butterfly
J Kvist, ALK Mattila, P Somervuo, V Ahola, P Koskinen, L Paulin, ...
Molecular Ecology 24 (19), 4886-4900, 2015
Complete genome sequence of Propionibacterium freudenreichii DSM 20271T
P Koskinen, P Deptula, OP Smolander, F Tamene, J Kammonen, ...
Standards in genomic sciences 10, 1-6, 2015
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
JP Koskinen, L Holm
Bioinformatics 28 (18), i438-i443, 2012
Transcriptome analysis reveals signature of adaptation to landscape fragmentation
P Somervuo, J Kvist, S Ikonen, P Auvinen, L Paulin, P Koskinen, L Holm, ...
PLoS One 9 (7), e101467, 2014
Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains
K Savijoki, A Iivanainen, P Siljamäki, PK Laine, L Paulin, T Karonen, ...
Journal of Proteome Research 13 (8), 3748-3762, 2014
Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1
O Niemi, P Laine, P Koskinen, M Pasanen, V Pennanen, H Harjunpää, ...
Standards in Genomic Sciences 12, 1-8, 2017
Genome sequence of Pectobacterium sp. strain SCC3193
JP Koskinen, P Laine, O Niemi, J Nykyri, H Harjunpää, P Auvinen, ...
Journal of bacteriology 194 (21), 6004-6004, 2012
Genomic features separating ten strains of Neorhizobium galegae with different symbiotic phenotypes
J Österman, SA Mousavi, P Koskinen, L Paulin, K Lindström
BMC genomics 16, 1-14, 2015
A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees
HX Ta, P Koskinen, L Holm
Bioinformatics 27 (5), 700-706, 2011
gapFinisher: a reliable gap filling pipeline for SSPACE-LongRead scaffolder output
JI Kammonen, OP Smolander, L Paulin, PAB Pereira, P Laine, ...
Plos one 14 (9), e0216885, 2019
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