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75 peer-reviewed articles • 4,508 peer-reviewed citations • Sorted by year • Download PDF (PDF by citations)
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1The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
Genome Research, 2025, 35, 475-488
3.29Citations (PDF)
2Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome
Animal Microbiome, 2025, 7, 65
2.510Citations (PDF)
3Protozoal populations drive system-wide variation in the rumen microbiome
Nature Communications, 2025, 16, 6238
11.016Citations (PDF)
4Linking genomic prediction of fillet fat content in Atlantic salmon to underlying changes in lipid metabolism regulation
Aquaculture, 2024, 584, 740678
3.43Citations (PDF)
5Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens
Communications Biology, 2024, 7, 1-19
3.112Citations (PDF)
6The genome regulatory landscape of Atlantic salmon liver through smoltification
PLoS ONE, 2024, 19, e0302388
1.510Citations (PDF)
7Integrating host and microbiome biology using holo-omics
Molecular Omics, 2024, 20, 438-452
1.616Citations (PDF)
8Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health
Nature Microbiology, 2024, 9, 1-16
10.230Citations (PDF)
9The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production
Communications Biology, 2024, 7, 1-10
3.115Citations (PDF)
10SOLA: dissecting dose-response patterns in multi-omics data using a semi-supervised workflow
Frontiers in Genetics, 2024, 15, 1508521
1.60Citations (PDF)
11Functional validation of transposable element-derived cis-regulatory elements in Atlantic salmon.
G3: Genes, Genomes, Genetics, 2023
1.44Citations (PDF)
12Metabolic influence of core ciliates within the rumen microbiome
ISME Journal, 2023, 17, 1128-1140
5.981Citations (PDF)
13A Dual Enrichment Strategy Provides Soil- and Digestate-Competent Nitrous Oxide-Respiring Bacteria for Mitigating Climate Forcing in Agriculture.
MBio, 2022, 13, e0078822
3.122Citations (PDF)
14What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?
Molecular Ecology, 2022, 31, 4271-4285
2.214Citations (PDF)
15Identification of growth regulators using cross-species network analysis in plants.
Plant Physiology, 2022, 190, 2350-2365
4.019Citations (PDF)
16Transkingdom network analysis provides insight into host-microbiome interactions in Atlantic salmon
Computational and Structural Biotechnology Journal, 2021, 19, 1028-1034
2.711Citations (PDF)
17Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
Biotechnology for Biofuels, 2021, 14, 1-14
6.414Citations (PDF)
18Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Genome Biology, 2021, 22, 1-18
4.886Citations (PDF)
19Innovation, conservation, and repurposing of gene function in root cell type development
Cell, 2021, 184, 3333-3348.e19
23.8112Citations (PDF)
20PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen
Cells, 2021, 10, 1971
3.422Citations (PDF)
21Leaf shape in Populus tremula is a complex, omnigenic trait
Ecology and Evolution, 2020, 10, 11922-11940
1.440Citations (PDF)
22Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut
Nature Communications, 2020, 11, 1-15
11.093Citations (PDF)
23Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes
Nature Communications, 2020, 11, 1-12
11.039Citations (PDF)
24A metabolite roadmap of the wood-forming tissue in Populus tremula
New Phytologist, 2020, 228, 1559-1572
5.353Citations (PDF)
25SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes
BMC Genomics, 2019, 20, 1-8
2.117Citations (PDF)
26Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae.
Plant Physiology, 2019, 180, 404-419
4.068Citations (PDF)
27Life-stage-associated remodelling of lipid metabolism regulation in Atlantic salmon
Molecular Ecology, 2018, 27, 1200-1213
2.247Citations (PDF)
28A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
BMC Genomics, 2018, 19, 1-18
2.132Citations (PDF)
29Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen
New Phytologist, 2018, 218, 999-1014
5.368Citations (PDF)
30The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication.
Genome Biology and Evolution, 2018, 10, 2785-2800
1.752Citations (PDF)
31Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Proceedings of the National Academy of Sciences of the United States of America, 2018, 115, E10970-E10978
5.3117Citations (PDF)
32From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus
ISME Journal, 2018, 13, 603-617
5.938Citations (PDF)
33NorWood: a gene expression resource for evo-devo studies of conifer wood development
New Phytologist, 2017, 216, 482-494
5.379Citations (PDF)
34Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
Genome Biology, 2017, 18, 1-14
4.8210Citations (PDF)
35AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula.
Plant Cell, 2017, 29, 1585-1604
5.8295Citations (PDF)
36Gene co-expression network connectivity is an important determinant of selective constraint
PLoS Genetics, 2017, 13, e1006402
2.2150Citations (PDF)
37Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development
BMC Genomics, 2016, 17, 1-17
2.142Citations (PDF)
38The Atlantic salmon genome provides insights into rediploidization
Nature, 2016, 533, 200-205
31.81,269Citations (PDF)
39Extracting functional trends from whole genome duplication events using comparative genomics
Biological Procedures Online, 2016, 18, 1-10
2.749Citations (PDF)
40Towards integration of population and comparative genomics in forest trees
New Phytologist, 2016, 212, 338-344
5.339Citations (PDF)
41Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)
PLoS ONE, 2015, 10, e0139080
1.531Citations (PDF)
42The Plant Genome Integrative Explorer Resource: PlantGenIE.org
New Phytologist, 2015, 208, 1149-1156
5.3348Citations (PDF)
43Populus tremula (European aspen) shows no evidence of sexual dimorphism
BMC Plant Biology, 2014, 14, 1-14
3.054Citations (PDF)
44ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa
BMC Genomics, 2014, 15, 1-17
2.175Citations (PDF)
45Genome interplay in the grain transcriptome of hexaploid bread wheat
Science, 2014, 345, 1250091
26.5374Citations (PDF)
46Synergy: A Web Resource for Exploring Gene Regulation in Synechocystis sp. PCC6803
PLoS ONE, 2014, 9, e113496
1.55Citations (PDF)
47Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in sp. PCC 6803 exposed to temperature and high light stress
Journal of Proteomics, 2013, 78, 294-311
1.920Citations (PDF)
48OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants
BMC Genomics, 2013, 14, 1-16
2.174Citations (PDF)
49Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica
BMC Genomics, 2013, 14, 1-12
2.142Citations (PDF)
50The Norway spruce genome sequence and conifer genome evolution
Nature, 2013, 497, 579-584
31.81,492Citations (PDF)
51Activity–dormancy transition in the cambial meristem involves stage-specific modulation of auxin response in hybrid aspen
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108, 3418-3423
5.3103Citations (PDF)
52A systems biology model of the regulatory network in Populusleaves reveals interacting regulators and conserved regulation
BMC Plant Biology, 2011, 11, 1-15
3.028Citations (PDF)
53Classification of microarrays; synergistic effects between normalization, gene selection and machine learning
BMC Bioinformatics, 2011, 12, 1-19
2.529Citations (PDF)
54Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
BMC Bioinformatics, 2010, 11, 1-14
2.556Citations (PDF)
55A Computer Scientist's Guide to the Regulatory Genome
Fundamenta Informaticae, 2010, 103, 323-332
0.22Citations (PDF)
56A Comprehensive Analysis of the Structure-Function Relationship in Proteins Based on Local Structure Similarity
PLoS ONE, 2009, 4, e6266
1.546Citations (PDF)
57Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.
Bioinformatics, 2009, 25, 1264-70
3.239Citations (PDF)
58Gene expression trends and protein features effectively complement each other in gene function prediction.
Bioinformatics, 2009, 25, 322-30
3.25Citations (PDF)
59Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions
Proteins: Structure, Function and Bioinformatics, 2009, 75, 870-884
1.917Citations (PDF)
60A segmental maximum a posteriori approach to genome-wide copy number profiling.
Bioinformatics, 2008, 24, 751-8
3.230Citations (PDF)
61Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space
Journal of Chemical Information and Modeling, 2008, 48, 2278-88
3.433Citations (PDF)
62Differential gene expression in the olfactory bulb following exposure to the olfactory toxicant 2,6-dichlorophenyl methylsulphone and its 2,5-dichlorinated isomer in mice
NeuroToxicology, 2007, 28, 1120-1128
2.41Citations (PDF)
63Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
BMC Systems Biology, 2007, 1, 1-17
2.88Citations (PDF)
64Generalized modeling of enzyme–ligand interactions using proteochemometrics and local protein substructures
Proteins: Structure, Function and Bioinformatics, 2006, 65, 568-579
1.940Citations (PDF)
65Discovering regulatory binding-site modules using rule-based learning
Genome Research, 2005, 15, 856-866
3.241Citations (PDF)
66A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins
Bioinformatics, 2004, 20, 293-293
3.28Citations (PDF)
67Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns
Genome Research, 2003, 13, 965-979
3.288Citations (PDF)
68Learning rule-based models of biological process from gene expression time profiles using gene ontology.
Bioinformatics, 2003, 19, 1116-23
3.282Citations (PDF)
69A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins.
Bioinformatics, 2003, 19 Suppl 2, ii81-91
3.228Citations (PDF)
70A transcriptional roadmap of the yearly growth cycle in Populus trees Open Access
Plant Cell, 0
5.84Citations (PDF)
71Gamma radiation-induced molecular toxicity and effects on pluripotent stem cells of the radiosensitive conifer Norway spruce (Picea abies)
Planta, 0, 262, 102
2.60Citations (PDF)
72Conservation of the short-day vernalization flowering response pathway in temperate Pooideae grasses
New Phytologist, 0, 251, 523-536
5.31Citations (PDF)
73OmniCorr: an R-package for visualizing putative host-microbiome interactions using multi-omics data.
Bioinformatics Advances, 0, 6, vbag057
0.90Citations (PDF)
74In vitro model reveals structural and metabolic insights into the porcine cecal microbiota in response to β-mannan exposure.
Applied and Environmental Microbiology, 0, 92, e0014026
2.40Citations (PDF)
75Comparative regulomics of wood formation across dicot and conifer trees.
Nature Communications, 0
11.02Citations (PDF)