Information till studenter och medarbetare med anledning av covid-19 (Uppdaterad: 20 januari 2021)

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Umeå universitet
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Personalbild Torgeir Hvidsten

Torgeir Hvidsten

Kontakt

E-post
torgeir.hvidsten@umu.se

Verksam vid

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

2020
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.
2020
PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline
Mannapperuma, Chanaka; Liu, H.; Bel, M.; et al.
2019
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.
2018
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.
2018
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.
2018
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.
2018
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.
2018
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.
2018
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.
2017
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.
2017
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.
2017
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.
2017
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.
2016
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.
2016
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.
2016
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.
2016
Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development
BMC Genomics, Vol. 17
Obudulu, Ogonna; Bygdell, Joakim; Sundberg, Bjorn; et al.
2016
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.
2015
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)
PLoS ONE, Vol. 10, (9)
Delhomme, Nicolas; Sundström, Görel; Zamani, Neda; et al.
2015
The Plant Genome Integrative Explorer Resource: PlantGenIE.org
New Phytologist, Vol. 208, (4) : 1149-1156
Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; et al.
2014
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.
2014
Populus tremula (European aspen) shows no evidence of sexual dimorphism
BMC Plant Biology, Vol. 14 : 276-
Robinson, Kathryn; Delhomme, Nicolas; Mahler, Niklas; et al.
2013
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.
2013
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.
2013
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.
2013
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.
2011
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.
2011
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
2011
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.
2010
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.
2009
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.
2009
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.
2009
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
2009
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.
2009
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.
2008
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.
Visa publikationer i DiVA