Torgeir Hvidsten

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Verksam vid

Anknuten som gästforskare till Institutionen för fysiologisk botanik Enhet: Umeå Plant Science Centre - associerad personal

KBC, Fysiologisk botanik, UPSC, C4-13-29 Umeå universitet, 901 87 Umeå

Forskning: Modellering av transkriptionella och metaboliska nätverk i träd, med hjälp av system biologi.

Vi integrerar beräkningsmässigt experimentella högdensitets data, från transkriptom-analys, metabolomik, proteomik och sekvensinformation, till nätverksmodeller för att beskriva samverkan mellan gener, proteiner och metaboliter, och de underliggande regulatoriska kopplingarna som är fastprogrammerade i trädets genome. Våra modeller, som bygger på maskininlärnings teknik, avslöjar allmänna trender i datat, och kan även predicera nya hypoteser för ytterligare experiment. Vi siktar på att uppnå synergieffekter mellan experimentell biologi och databiologi genom iterativt använda modeller för att styra experimentalister och nya experimentella resultat för att förbättra modellerna.

För mera detaljerad information, Torgeir Hvidsten@UPSC

Overexpression 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, BioMed Central 2021, Vol. 14, (1)

Gandla, Madhavi Latha; Mähler, Niklas; Escamez, Sacha; et al.

A metabolite roadmap of the wood-forming tissue in Populus tremula

New Phytologist, John Wiley & Sons 2020, Vol. 228, (5) : 1559-1572

Abreu, Ilka N.; Johansson, Annika I.; Sokolowska, Katarzyna; et al.

PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline

Mannapperuma, Chanaka; Liu, H.; Bel, M.; et al.

Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae

Plant Physiology, American Society of Plant Biologists 2019, Vol. 180, (1) : 404-419

Schubert, Marian; Gronvold, Lars; Sandve, Simen R.; et al.

Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen

New Phytologist, Vol. 218, (3) : 999-1014

Felten, Judith; Vahala, Jorma; Love, Jonathan; et al.

Functional 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, NATL ACAD SCIENCES 2018, Vol. 115, (46) : E10970-E10978

Lin, Yao-Cheng; Wang, Jing; Delhomme, Nicolas; et al.

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees

BMC Genomics, Springer Publishing Company 2018, Vol. 19

Obudulu, Ogonna; Mähler, Niklas; Skotare, Tomas; et al.

Subfunctionalization versus neofunctionalization after whole-genome duplication

Nature Genetics, Nature Publishing Group 2018, Vol. 50, (7) : 908-909

Sandve, Simen R.; Rohlfs, Rori V.; Hvidsten, Torgeir R.

Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication

Science, American Association for the Advancement of Science (AAAS) 2018, Vol. 360, (6385) : 212-214

Tylewicz, S.; Petterle, A.; Marttila, S.; et al.

The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication

Genome Biology and Evolution, Oxford University Press 2018, Vol. 10, (10) : 2785-2800

Varadharajan, Srinidhi; Sandve, Simen R.; Gillard, Gareth B.; et al.

NorWood: a gene expression resource for evo-devo studies of conifer wood development

New Phytologist, Vol. 216, (2) : 482-494

Jokipii-Lukkari, Soile; Sundell, David; Nilsson, Ove; et al.

Gene co-expression network connectivity is an important determinant of selective constraint

PLoS Genetics, PUBLIC LIBRARY SCIENCE 2017, Vol. 13, (4)

Mähler, Niklas; Wang, Jing; Terebieniec, Barbara K.; et al.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

Genome Biology, BioMed Central 2017, Vol. 18

Robertson, Fiona M.; Gundappa, Manu Kumar; Grammes, Fabian; et al.

AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula

The Plant Cell, Vol. 29, (7) : 1585-1604

Sundell, David; Street, Nathaniel R.; Kumar, Manoj; et al.

Extracting functional trends from whole genome duplication events using comparative genomics

Biological Procedures Online, Vol. 18

Hermansen, Russell A.; Hvidsten, Torgeir R.; Sandve, Simen Rod; et al.

Towards integration of population and comparative genomics in forest trees

New Phytologist, Vol. 212, (2) : 338-344

Ingvarsson, Pär K.; Hvidsten, Torgeir R.; Street, Nathaniel R.

The Atlantic salmon genome provides insights into rediploidization

Nature, Nature Publishing Group 2016, Vol. 533, (7602) : 200-205

Lien, Sigbjorn; Koop, Ben F.; Sandve, Simen R.; et al.

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development

BMC Genomics, Vol. 17

Obudulu, Ogonna; Bygdell, Joakim; Sundberg, Bjorn; et al.

High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula

Sundell, David; Street, Nathaniel R; Kumar, Manoj; et al.

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)

PLoS ONE, Vol. 10, (9)

Delhomme, Nicolas; Sundström, Görel; Zamani, Neda; et al.

The Plant Genome Integrative Explorer Resource: PlantGenIE.org

New Phytologist, Vol. 208, (4) : 1149-1156

Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; et al.

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

BMC Genomics, Vol. 15 : 106-

Netotea, Sergiu; Sundell, David; Street, Nathaniel R.; et al.

Populus tremula (European aspen) shows no evidence of sexual dimorphism

BMC Plant Biology, Vol. 14 : 276-

Robinson, Kathryn; Delhomme, Nicolas; Mahler, Niklas; et al.

Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica

BMC Genomics, BioMed Central 2013, Vol. 14 : 885-

Immanen, Juha; Nieminen, Kaisa; Duchens Silva, Hector; et al.

Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in Synechocystis sp. PCC 6803 exposed to temperature and high light stress

Journal of Proteomics, Elsevier 2013, Vol. 78 : 294-311

Miranda, Helder; Charegi, Otilia; Netotea, Sergiu; et al.

The Norway spruce genome sequence and conifer genome evolution

Nature, Nature Publishing Group 2013, Vol. 497, (7451) : 579-584

Nystedt, Björn; Street, Nathaniel Robert; Wetterbom, Anna; et al.

OnPLS 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, BioMed Central 2013, Vol. 14

Srivastava, Vaibhav; Obudulu, Ogonna; Bygdell, Joakim; et al.

Activity-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, Vol. 108, (8) : 3418-23

Baba, Kyoko; Karlberg, Anna; Schmidt, Julien; et al.

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation

BMC Plant Biology, Vol. 11 : 13-

Street, Nathaniel Robert; Jansson, Stefan; Hvidsten, Torgeir

Classification of microarrays: synergistic effects between normalization, gene selection and machine learning

BMC Bioinformatics, BioMed Central 2011, Vol. 12, (1)

Önskog, Jenny; Freyhult, Eva; Landfors, Mattias; et al.

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering

BMC Bioinformatics, BioMed Central 2010, Vol. 11

Freyhult, Eva; Landfors, Mattias; Önskog, Jenny; et al.

Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.

Bioinformatics, Vol. 25, (10) : 1264-1270

Björkholm, Patrik; Daniluk, Pawel; Kryshtafovych, Andriy; et al.

Bioinformatics strategies for cDNA-microarray data processing

Batch effects and noise in microarray experiments: sources and solutions, Wiley and Sons 2009 : 61-74

Fahlén, Jessica; Landfors, Mattias; Freyhult, Eva; et al.

Local 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, Vol. 75, (4) : 870-884

Hvidsten, Torgeir; Kryshtafovych, Andriy; Fidelis, Krzysztof

A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity

PLoS ONE, Vol. 4, (7) : e6266-

Hvidsten, Torgeir; Laegreid, Astrid; Kryshtafovych, Andriy; et al.

Gene expression trends and protein features effectively complement each other in gene function prediction

Bioinformatics, Vol. 25, (3) : 322-330

Wabnik, Krzysztof; Hvidsten, Torgeir; Kedzierska, Anna; et al.

Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space.

Journal of Chemical Information and Modeling, Vol. 48 : 2278-2288

Strombergsson, Helena; Daniluk, Pawel; Kryshtafovych, Andriy; et al.

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