Publications

2026

  1. Chaudhary, S., Piombo, E., Dubey, M., Jensen, D. F., Grenville-Briggs, L. and Karlsson, M. (2026). Transcriptomic analysis of two wheat genotypes in the presence of the pathogen zymoseptoria tritici and the biological control agent clonostachys rosea [Article]. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY, 141. https://doi.org/10.1016/j.pmpp.2025.103013

2025

  1. Alemu, A., Anguluri, K., Yuan, B., Lametsch, R. and Hammenhag, C. (2025). Genetic variation in storage protein and starch biosynthesis genes reveals key associations with seed composition in pea (pisum sativum). Frontiers in Plant Science. https://doi.org/10.3389/fpls.2025.1679498
  2. Bengtsson, F., Cronberg, N., Lozano Villegas, J. A., Siddique, A. B., Stenberg, P. and Ekroos, J. (2025). Rapid shifts in bryophyte phenology revealed by airborne eDNA. Journal of Ecology. https://doi.org/10.1111/1365-2745.70180
  3. Bergholm, J., Tessema, T. S., Blomstroem, A.-L. and Berg, M. (2025). Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from ethiopia [Article]. VIROLOGY JOURNAL, 22(1). https://doi.org/10.1186/s12985-025-02821-8
  4. Chekole, W. S., Potgieter, L., Adamu, H., Sternberg-Lewerin, S., Tessema, T. S. and Magnusson, U. (2025). Genomic insights into antimicrobial resistance and virulence of e. Coli in central ethiopia: A one health approach [Article]. FRONTIERS IN MICROBIOLOGY, 16. https://doi.org/10.3389/fmicb.2025.1597580
  5. Choudhary, S., Renström, A., Kochakarn, T., Piombo, E., Miskolczi, P., Jämtgård, S., Henriksson, J. and Tuominen, H. (2025). Tracing the dynamics of nitrate responses in xylem elements of hybrid aspen wood [Preprint]. Research Square. https://doi.org/10.21203/rs.3.rs-7685028/v1
  6. Cojkic, A., Niazi, A., Hansson, I. and Morrell, J. M. (2025). Variations in bacterial profiles associated with semen collection timing and bull breed, analyzed using 16S rRNA sequencing and MALDI-TOF MS [Article]. FRONTIERS IN VETERINARY SCIENCE, 12. https://doi.org/10.3389/fvets.2025.1583136
  7. Derba-Maceluch, M., Garcı́a Romañach, L., Hedenström, M., Mitra, M., Donev, E. N., Urbancsok, J., Yassin, Z., Gandla, M. L., Sivan, P., Šimura, J., et al. (2025). Glucuronoyl esterase expressed in aspen xylem affects \(\gamma\)-ester linkages between lignin and glucuronoxylan reducing recalcitrance and accelerating growth. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.70301
  8. Hossein Banabazi, M., Van Borm, S., Klingstrom, T., Niazi, A., De Clercq, K., Mostin, L., Haegeman, A. and Koning, D. J. de. (2025). Host transcriptome profiling for resistance against lumpy skin disease (LSD) [Article]. BMC RESEARCH NOTES, 18(1). https://doi.org/10.1186/s13104-025-07388-9
  9. Hvidsten, T., Rodriguez, E., Birkeland, S., Chapple, E., Fredriksson, S., Lorenzo, Z., Kalman, T., Kumar, V., Mccann, J., Hill, J., et al. (2025). An evo-devo resource for wood: Comparative regulomics across dicot and conifer trees [Preprint]. Research Square. https://doi.org/10.21203/rs.3.rs-7656402/v1
  10. Landi, M., Carluccio, A. V., Shah, T., Niazi, A., Stavolone, L., Falquet, L., Gisel, A. and Bongcam-Rudloff, E. (2025). Genome-wide comparison reveals large structural variants in cassava landraces [Article]. BMC GENOMICS, 26(1). https://doi.org/10.1186/s12864-025-11523-y
  11. Marcon, A., Romañach, L. G., André, D., Ding, J., Zhang, B., Hvidsten, T. R. and Nilsson, O. (2025). A transcriptional roadmap of the yearly growth cycle in populus trees. The Plant Cell, 37(9), koaf208. p. https://doi.org/10.1093/plcell/koaf208
  12. Puthanveed, V., Sajeevan, R. S., Siddique, A. B., Alexandersson, E., Joshi, P., Snell, P., Lennefors, B.-L. and Kvarnheden, A. (2025). Transcriptomic responses of beet to infection by beet mild yellowing virus [Article]. BMC PLANT BIOLOGY, 25(1). https://doi.org/10.1186/s12870-025-07514-6
  13. Quevedo, M., Kubalova, I., Brun, A., Cervela-Cardona, L., Monte, E. and Strand, A. (2025). Retrograde signals control dynamic changes to the chromatin state at photosynthesis-associated loci [Article]. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-61831-w
  14. Rodriguez, E., Birkeland, S., Chapple, E. D., Fredriksson, S., Lorenzo, Z. C., Kalman, T. A., Kumar, V., Hill, J., Tuominen, H., Mellerowicz, E. J., et al. (2025). Comparative regulomics provides novel insight into the evolution of wood formation across dicot and conifer trees [Preprint]. bioRxiv, 2025–2006. pp.
  15. Schneider, A. N., Buckley, S., Lorenzo, Z. C., Gratz, R., Nilsson, L., Swaine, M., Street, N. R., Taylor, A. F. and Jämtgård, S. (2025). Reverse microdialysis of sucrose stimulates soil fungal and bacterial growth at the microscale. BMC Microbiology, 25(1), 436. p. https://doi.org/10.1186/s12866-025-04082-5
  16. Schwochow, D., Alameddine, A., Sporndly-Nees, E., Montigny, M., Naboulsi, R., Jansson, A., Niazi, A. and Lindgren, G. (2025). RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in standardbred trotters [Article]. BMC GENOMICS, 26(1). https://doi.org/10.1186/s12864-025-11814-4
  17. Sigurdardottir, H., Eriksson, S., Niazi, A., Rhodin, M., Albertsdottir, E., Kristjansson, T. and Lindgren, G. (2025). Genetic influence of a STAU2 frameshift mutation and RELN regulatory elements on performance in icelandic horses [Article]. SCIENTIFIC REPORTS, 15(1). https://doi.org/10.1038/s41598-025-95593-8
  18. Sivan, P., Urbancsok, J., Donev, E. N., Derba-Maceluch, M., Barbut, F. R., Yassin, Z., Gandla, M. L., Mitra, M., Heinonen, S. E., Simura, J., Cermanova, K., Karady, M., Scheepers, G., Jonsson, L. J., Master, E. R., Vilaplana, F. and Mellerowicz, E. J. (2025). Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs and improves saccharification [Article]. PLANT BIOTECHNOLOGY JOURNAL, 23(1), 174–197. pp. https://doi.org/10.1111/pbi.14487
  19. Taliadoros, D., Potgieter, L., Dhiman, A., Wyatt, N. A., McMullan, M., Jung, C., Bolton, M. D. and Stukenbrock, E. H. (2025). Genome-wide evidence of host specialization in wild and farmland populations of the fungal leaf spot pathogen, cercospora beticola [Article]. GENOME BIOLOGY AND EVOLUTION, 17(4). https://doi.org/10.1093/gbe/evaf053
  20. Urbancsok, J., Donev, E. N., Derba-Maceluch, M., Sivan, P., Barbut, F. R., Mitra, M., Yassin, Z., Cermanová, K., Šimura, J., Karady, M., et al. (2025). Wood-specific modification of glucuronoxylan can enhance growth in populus. Journal of Experimental Botany, eraf364. p. https://doi.org/10.1093/jxb/eraf364
  21. Vergara, A., Hernández-Verdeja, T., Ojeda-May, P., Ramirez, L., Edler, D., Rosvall, M. and Strand, A. (2025). IsoformMapper: A web application for protein-level comparison of splice variants through structural community analysis [Preprint]. bioRxiv. https://doi.org/10.1101/2025.03.05.641708
  22. Vittozzi, Y., Petri, L., Chiurazzi, M. J., Lisón, P., Hernández, C. G., Majee, A., Shankar, N., Burow, M. and Wenkel, S. (2025). Antagonistic and synergistic roles of tomato AFP3 isoforms in hormonal regulation and development. bioRxiv, 2025–2006. pp. https://doi.org/10.1101/2025.06.18.660365
  23. Zacharaki, V., Quevedo, M., Nardeli, S. M., Meena, S. K., Monte, E. and Kindgren, P. (2025). Convergent antisense transcription primes hosting genes for stress responsiveness in plants. Molecular Plant, 18(11), 1920–1931. pp. https://doi.org/10.1016/j.molp.2025.10.001
  24. Zhang, Y., Choudhary, S., Renström, A., Luomaranta, M., Chantreau, M., Fleig, V., Gaboreanu, I., Grones, C., Nilsson, O., Robinson, K. M., et al. (2025). Unraveling nitrogen uptake and metabolism: Gene families, expression dynamics and functional insights in aspen (populus tremula). Tree Physiology, tpaf099. p. https://doi.org/10.1093/treephys/tpaf099

2024

  1. Abdel-Fattah, W. R., Carlsson, M., Hu, G.-Z., Singh, A., Vergara, A., Aslam, R., Ronne, H. and Bjoerklund, S. (2024). Growth-regulated co-occupancy of mediator and Lsm3 at intronic ribosomal protein genes [Article]. Nucleic Acids Research, 52(11), 6220–6233. pp. https://doi.org/10.1093/nar/gkae266
  2. Ayalew, W., Wu, X., Tarekegn, G. M., Sisay Tessema, T., Naboulsi, R., Van Damme, R., Bongcam-Rudloff, E., Edea, Z., Chu, M., Enquahone, S., Liang, C. and Yan, P. (2024). Whole genome scan uncovers candidate genes related to milk production traits in barka cattle [Article]. International Journal of Molecular Sciences, 25(11). https://doi.org/10.3390/ijms25116142
  3. Ayalew, W., Wu, X., Tarekegn, G. M., Tessema, T. S., Chu, M., Liang, C., Naboulsi, R., Van Damme, R., Bongcam-Rudloff, E. and Ping, Y. (2024). Whole-genome sequencing of copy number variation analysis in ethiopian cattle reveals adaptations to diverse environments [Article]. BMC GENOMICS, 25(1). https://doi.org/10.1186/s12864-024-10936-5
  4. Ayalew, W., Xiaoyun, W., Tarekegn, G. M., Naboulsi, R., Tessema, T. S., Van Damme, R., Bongcam-Rudloff, E., Chu, M., Liang, C., Edea, Z., Enquahone, S. and Ping, Y. (2024). Whole genome sequences of 70 indigenous ethiopian cattle [Article]. Scientific Data, 11(1). https://doi.org/10.1038/s41597-024-03342-9
  5. Banabazi, M. H., Freimanis, G., Goatley, L. C., Netherton, C. L. and Koning, D.-J. de. (2024). The transcriptomic insight into the differential susceptibility of african swine fever in inbred pigs [Article]. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-56569-2
  6. Barcala, M. E., Valk, T. van der, Chen, Z., Funda, T., Chaudhary, R., Klingberg, A., Fundova, I., Suontama, M., Hallingback, H., Bernhardsson, C., Nystedt, B., Ingvarsson, P. K., Sherwood, E., Street, N., Gyllensten, U., Nilsson, O. and Wu, H. X. (2024). Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for scots pine (pinus sylvestris l.) and its transferability to other pine species [Article]. Plant Journal, 117(3), 944–955. pp. https://doi.org/10.1111/tpj.16535
  7. Bhat, S. S., Asgari, M., Mermet, S., Mishra, P. and Kindgren, P. (2024). The nuclear exosome subunit HEN2 acts independently of the core exosome to assist transcription in arabidopsis. Plant Physiology, 196(4), 2625–2637. pp. https://doi.org/10.1093/plphys/kiae503
  8. Canovi, C., Stojkovič, K., Benı́tez, A. A., Delhomme, N., Egertsdotter, U. and Street, N. R. (2024). A resource of identified and annotated lincRNAs expressed during somatic embryogenesis development in norway spruce. Physiologia Plantarum, 176(5), e14537. p. https://doi.org/10.1111/ppl.14537
  9. Cojkic, A., Niazi, A. and Morrell, J. M. (2024). Metagenomic identification of bull semen microbiota in different seasons [Article]. Animal Reproduction Science, 268. https://doi.org/10.1016/j.anireprosci.2024.107569
  10. Dube, F., Delhomme, N., Martin, F., Hinas, A., Åbrink, M., Svärd, S. and Tydén, E. (2024). Gene co-expression network analysis reveal core responsive genes in parascaris univalens tissues following ivermectin exposure [Article]. PLoS One, 19(2). https://doi.org/10.1371/journal.pone.0298039
  11. El Arbi, N., Nardeli, S. M., Šimura, J., Ljung, K. and Schmid, M. (2024). The arabidopsis splicing factor PORCUPINE/SmE1 orchestrates temperature-dependent root development via auxin homeostasis maintenance. New Phytologist, 244(4), 1408–1421. pp. https://doi.org/10.1111/nph.20153
  12. Hermann, E., Van Damme, R., Bongcam-Rudloff, E. and Nasirzadeh, L. (2024). Urban pigeons as reservoirs of critical pathogens: Improved protocol for sequencing pigeon faeces in disease monitoring. EMBnet. Journal, 30, 1059. p. https://doi.org/10.14806/ej.30.0.1059
  13. Hermida-Carrera, C., Vergara, A., Cervela-Cardona, L., Jin, X., Björklund, S. and Strand, Å. (2024). CDK8 of the mediator kinase module connects leaf development to the establishment of correct stomata patterning by regulating the levels of the transcription factor SPEECHLESS (SPCH). Plant, Cell & Environment, 47(12), 5237–5251. pp. https://doi.org/10.1111/pce.15102
  14. Islam, M. M., Deepo, D. M., Siddique, A. B., Nasif, S. O., Zonayet, M., Hassan, O., Siddique, A. B. and Ali, M. A. (2024). B chromosomes in wheat: Evolution, functions and breeding potential. Agronomy, 14(11). https://doi.org/10.3390/agronomy14112682
  15. Jhamat, N., Guo, Y., Han, J., Humblot, P., Bongcam-Rudloff, E., Andersson, G. and Niazi, A. (2024). Enrichment of cis-acting regulatory elements in differentially methylated regions following lipopolysaccharide treatment of bovine endometrial epithelial cells [Article]. International Journal of Molecular Sciences, 25(18). https://doi.org/10.3390/ijms25189832
  16. Lazaro-Gimeno, D., Ferrari, C., Delhomme, N., Johansson, M., Sjolander, J., Singh, R. K., Mutwil, M. and Eriksson, M. E. (2024). The circadian clock participates in seasonal growth in norway spruce (picea abies) [Article]. Tree Physiology, 44(11). https://doi.org/10.1093/treephys/tpae139
  17. Luomaranta, M., Grones, C., Choudhary, S., Milhinhos, A., Kalman, T. A., Nilsson, O., Robinson, K. M., Street, N. R. and Tuominen, H. (2024). Systems genetic analysis of lignin biosynthesis in populus tremula [Article]. New Phytologist, 243(6), 2157–2174. pp. https://doi.org/10.1111/nph.19993
  18. Malaluang, P., Niazi, A., Guo, Y., Nagel, C., Guimaraes, T., Rocha, A., Aurich, C. and Morrell, J. M. (2024). Bacterial diversity in semen from stallions in three european countries evaluated by 16S sequencing [Article]. Veterinary Research Communications, 48(3), 1409–1421. pp. https://doi.org/10.1007/s11259-024-10321-3
  19. Manourova, A., Polesny, Z., Ruiz-Chutan, A., Sillam-Dusses, D., Tsafack, S., Tchoudjeu, Z., Potgieter, L. and Lojka, B. (2024). Identification of plus trees for domestication: Phenotypical description of garcinia kola populations in cameroon. Genetic Recourses and Crop Evolution, 71(8), 1893–1909. pp. https://doi.org/10.1007/s10722-023-01750-1
  20. Meena, S. K., Quevedo, M., Nardeli, S. M., Verez, C., Bhat, S. S., Zacharaki, V. and Kindgren, P. (2024). Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in arabidopsis. The Plant Cell, 36(9), 3467–3482. pp. https://doi.org/10.1093/plcell/koae160
  21. Nardeli, S. M., El Arbi, N., Dikaya, V., Rojas-Murcia, N., Goretti, D. and Schmid, M. (2024). Time and temperature-resolved transcriptomic analysis of arabidopsis splicing-related mutants [Preprint]. bioRxiv, 2024–2011. pp. https://doi.org/10.1101/2024.11.08.622454
  22. Ohm, H., Saripella, G. V., Hofvander, P. and Grimberg, A. (2024). Spatio-temporal transcriptome and storage compound profiles of developing faba bean (vicia faba) seed tissues [Article]. Frontiers in Plant Science, 15. https://doi.org/10.3389/fpls.2024.1284997
  23. Resjo, S., Willforss, J., Large, A., Siino, V., Alexandersson, E., Levander, F. and Andreasson, E. (2024). Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days [Article]. Plant Physiology and Biochemistry, 215. https://doi.org/10.1016/j.plaphy.2024.109032
  24. Robinson, K. M., Schiffthaler, B., Liu, H., Rydman, S. M., Rendon-Anaya, M., Kalman, T. A., Kumar, V., Canovi, C., Bernhardsson, C., Delhomme, N., Jenkins, J., Wang, J., Mahler, N., Richau, K. H., Stokes, V., A’Hara, S., Cottrell, J., Coeck, K., Diels, T., … Street, N. R. (2024a). An improved chromosome-scale genome assembly and population genetics resource for populus tremula [Article]. Physiologia Plantarum, 176(5). https://doi.org/10.1111/ppl.14511
  25. Robinson, K. M., Schiffthaler, B., Liu, H., Rydman, S. M., Rendon-Anaya, M., Kalman, T. A., Kumar, V., Canovi, C., Bernhardsson, C., Delhomme, N., Jenkins, J., Wang, J., Mahler, N., Richau, K. H., Stokes, V., A’Hara, S., Cottrell, J., Coeck, K., Diels, T., … Street, N. R. (2024b). Correction to an improved chromosome-scale genome assembly and population genetics resource for populus tremula [Correction]. Physiologia Plantarum, 176(5). https://doi.org/10.1111/ppl.14564
  26. Sibhat, B., Adamu, H., Asmare, K., Lindahl, J. F., Magnusson, U. and Sisay Tessema, T. (2024). Detection and molecular diversity of brucella melitensis in pastoral livestock in north-eastern ethiopia. Pathogens, 13(12), 1063. p. https://doi.org/10.3390/pathogens13121063
  27. Siddique, A. B., Maharwa, L. and Albrectsen, B. (2024). Genotype, tannin capacity, and seasonality influence the structure and function of symptomless fungal communities in aspen leaves, regardless of historical nitrogen addition [Preprint]. Research Square. https://doi.org/10.21203/rs.3.rs-4206868/v1
  28. Spain, O., Bajhaiya, A. K., Tanner, H., Cook, S. and Funk, C. (2024). Transcriptomic analysis of a cold-resistant nordic microalga: Unraveling the mechanisms underlying adaptation to low temperatures. Physiologia Plantarum, 176(3), e14402. p. https://doi.org/10.1111/ppl.14402
  29. Stojkovič, K., Canovi, C., Le, K.-C., Ahmad, I., Gaboreanu, I., Johansson, S., Delhomme, N., Egertsdotter, U. and Street, N. R. (2024). A transcriptome atlas of zygotic and somatic embryogenesis in norway spruce [Article]. Plant Journal, 120(5), 2238–2252. pp. https://doi.org/10.1111/tpj.17087
  30. Street, N., Nystedt, B., Delhomme, N., Eriksson, M. C., Hill, J., Ahlgren Kalman, T., Kumar, V., Larsson, T., Nandi, S., Mähler, N., et al. (2024). New genome insights from chromosome-scale genome assemblies of norway spruce (picea abies) and scots pine (pinus sylvestris) [Preprint]. Umeå Universitet, Diva.

2023

  1. Ayalew, W., Wu, X., Tarekegn, G. M., Sisay Tessema, T., Naboulsi, R., Van Damme, R., Bongcam-Rudloff, E., Edea, Z., Enquahone, S. and Yan, P. (2023). Whole-genome resequencing reveals selection signatures of abigar cattle for local adaptation [Article]. ANIMALS, 13(20). https://doi.org/10.3390/ani13203269
  2. Bai, B., Schiffthaler, B., Horst, S. van der, Willems, L., Vergara, A., Karstrom, J., Mahler, N., Delhomme, N., Bentsink, L. and Hanson, J. (2023). SeedTransNet: A directional translational network revealing regulatory patterns during seed maturation and germination [Article]. Journal of Experimental Botany, 74(7, SI), 2416–2432. pp. https://doi.org/10.1093/jxb/erac394
  3. Belda-Perez, R., Heras, S., Cimini, C., Romero-Aguirregomezcorta, J., Valbonetti, L., Colosimo, A., Maria Colosimo, B., Santoni, S., Bernabo, N., Coy, P., et al. (2023). Effects of a polycaprolactone and polyethylene glycol diacrylate, 3-d printed scaffolds, on bovine embryo development in vitro. Animal Reproduction, 20(2), 8–8. pp. https://re.public.polimi.it/retrieve/6fb345c3-60a5-4236-a703-786e4ac1551a/AETE%202023.pdf
  4. Bhat, S. S., Bielewicz, D. and Kindgren, P. (2023). MTA influences RNA polymerase II transcription dynamics and regulates the cold response in arabidopsis [Preprint]. bioRxiv, 2023–2005. pp. https://doi.org/10.1101/2023.05.10.540235
  5. Dube, F., Hinas, A., Delhomme, N., abrink, M., Svard, S. and Tyden, E. (2023). Transcriptomics of ivermectin response in caenorhabditis elegans: Integrating abamectin quantitative trait loci and comparison to the ivermectin-exposed DA1316 strain [Article]. PLoS One, 18(5). https://doi.org/10.1371/journal.pone.0285262
  6. Eilertsen, L., Hultberg, M., Lee, N., Saroj, P., Swaine, M., Chen, F. and Xiong, S. (2023). The microbial community in a substrate of solid-state fermentation by lentinula edodes: A preliminary study. Fermentation, 9(8), 736. p. https://doi.org/10.3390/fermentation9080736
  7. Galmiche, M., Sonnette, A., Wolf, M., Sutter, C., Delhomme, O., Francois, Y.-N. and Millet, M. (2023). Simultaneous determination of 79 polar and non-polar polycyclic aromatic compounds in airborne particulate matter by gas chromatography - tandem mass spectrometry [Article]. Polycyclic Aromatic Compounds, 43(10), 8841–8860. pp. https://doi.org/10.1080/10406638.2022.2153884
  8. Gisel, A., Stavolone, L., Olagunju, T., Landi, M., Damme, R. van, Niazi, A., Falquet, L., Shah, T. and Bongcam-Rudloff, E. (2023). EpiCass and CassavaNet4Dev advanced bioinformatics workshop. EMBnet.journal, 29(0), 1045. p. https://doi.org/10.14806/ej.29.0.1045
  9. Hemberg, E., Niazi, A., Guo, Y., Debnar, V. J., Vincze, B., Morrell, J. M. and Kutvolgyi, G. (2023). Microbial profiling of amniotic fluid, umbilical blood and placenta of the foaling mare [Article]. Animals, 13(12). https://doi.org/10.3390/ani13122029
  10. Landi, M., Shah, T., Falquet, L., Niazi, A., Stavolone, L., Bongcam-Rudloff, E. and Gisel, A. (2023). Haplotype-resolved genome of heterozygous african cassava cultivar TMEB117 (manihot esculenta) [Article; Data Paper]. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02800-0
  11. Lihavainen, J., Simura, J., Bag, P., Fataftah, N., Robinson, K. M., Delhomme, N., Novak, O., Ljung, K. and Jansson, S. (2023). Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature [Article]. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-39564-5
  12. Nardeli, S. M., Zacharaki, V., Rojas-Murcia, N., Collani, S., Wang, K., Bayer, M., Schmid, M. and Goretti, D. (2023). Arabidopsis thaliana LSM7 is essential for auxin-mediated regulation of SAUR genes and thermomorphogenesis [Preprint]. bioRxiv, 2023–2003. pp. https://doi.org/10.1101/2023.03.28.534379
  13. Puthanveed, V., Singh, K., Poimenopoulou, E., Pettersson, J., Siddique, A. B. and Kvarnheden, A. (2023). Milder autumns may increase risk for infection of crops with turnip yellows virus [Article]. PHYTOPATHOLOGY, 113(9), 1788–1798. pp. https://doi.org/10.1094/PHYTO-11-22-0446-V
  14. Sajeevan, R. S., Abdelmeguid, I., Saripella, G. V., Lenman, M. and Alexandersson, E. (2023). Comprehensive transcriptome analysis of different potato cultivars provides insight into early blight disease caused by alternaria solani. BMC Plant Biology, 23(1), 130. p. https://doi.org/10.1186/s12870-023-04135-9
  15. Schiffthaler, B., Zalen, E. van, Serrano, A. R., Street, N. R. and Delhomme, N. (2023). Seiðr: Efficient calculation of robust ensemble gene networks [Article]. HELIYON, 9(6). https://doi.org/10.1016/j.heliyon.2023.e16811
  16. Stenberg, H., Malmberg, M. and Hayer, J. (2023). Screening for atypical porcine pestivirus in swedish boar semen used for artificial insemination and a characterisation of the seminal RNA microbiome including the virome [Article]. BMC Veterinary Research, 19(1). https://doi.org/10.1186/s12917-023-03762-6
  17. Sullivan, A. R., Karlsson, E., Svensson, D., Brindefalk, B., Villegas, J. A., Mikko, A., Bellieny, D., Siddique, A. B., Johansson, A.-M., Grahn, H., Sundell, D., Norman, A., Esseen, P.-A., Sjödin, A., Singh, N. J., Brodin, T., Forsman, M. and Stenberg, P. (2023). Airborne eDNA captures three decades of ecosystem biodiversity. bioRxiv. https://doi.org/10.1101/2023.12.06.569882
  18. Urbancsok, J., Donev, E. N., Sivan, P., Zalen, E. van, Barbut, F. R., Derba-Maceluch, M., Simura, J., Yassin, Z., Gandla, M. L., Karady, M., Ljung, K., Winestrand, S., Jonsson, L. J., Scheepers, G., Delhomme, N., Street, N. R. and Mellerowicz, E. J. (2023). Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development [Article]. New Phytologist, 240(6), 2312–2334. pp. https://doi.org/10.1111/nph.19307

2022

  1. Akhter, S., Westrin, K. J., Zivi, N., Nordal, V., Kretzschmar, W. W., Delhomme, N., Street, N. R., Nilsson, O., Emanuelsson, O. and Sundstrom, J. F. (2022). Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway [Article]. New Phytologist, 236(5), 1951–1963. pp. https://doi.org/10.1111/nph.18449
  2. André, D., Marcon, A., Lee, K. C., Goretti, D., Zhang, B., Delhomme, N., Schmid, M. and Nilsson, O. (2022). FLOWERING LOCUS t paralogs control the annual growth cycle in populus trees. Current Biology, 32(13), 2988–2996. pp. https://doi.org/https://doi.org/10.1016/j.cub.2022.05.023
  3. Balinandi, S., Hayer, J., Cholleti, H., Wille, M., Lutwama, J. J., Malmberg, M. and Mugisha, L. (2022). Identification and molecular characterization of highly divergent RNA viruses in cattle, uganda. Virus Research, 313, 198739. p. https://doi.org/https://doi.org/10.1016/j.virusres.2022.198739
  4. Boussardon, C., Bag, P., Juvany, M., Simura, J., Ljung, K., Jansson, S. and Keech, O. (2022). The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence [Article]. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03998-2
  5. Castro, D., Concha, C., Jamett, F., Ibanez, C. and Hurry, V. (2022). Soil microbiome influences on seedling establishment and growth of prosopis chilensis and prosopis tamarugo from northern chile [Article]. PLANTS-BASEL, 11(20). https://doi.org/10.3390/plants11202717
  6. Cholleti, H., Jong, J. de, Blomström, A.-L. and Berg, M. (2022a). Characterization of pipistrellus pygmaeus bat virome from sweden. Viruses, 14(8), 1654. p. https://doi.org/10.3390/v14081654
  7. Cholleti, H., Jong, J. de, Blomström, A.-L. and Berg, M. (2022b). Investigation of the virome and characterization of issyk-kul virus from swedish myotis brandtii bats. Pathogens, 12(1), 12. p.
  8. Chowdhury, J., Kemppainen, M., Delhomme, N., Shutava, I., Zhou, J., Takahashi, J., Pardo, A. G. and Lundberg-Felten, J. (2022). Laccaria bicolor pectin methylesterases are involved in ectomycorrhiza development with populus tremula x populus tremuloides [Article]. New Phytologist, 236(2), 639–655. pp. https://doi.org/10.1111/nph.18358
  9. Dube, F., Hinas, A., Roy, S., Martin, F., Åbrink, M., Svärd, S. and Tydén, E. (2022). Ivermectin-induced gene expression changes in adult parascaris univalens and caenorhabditis elegans: A comparative approach to study anthelminthic metabolism and resistance in vitro. Parasites & Vectors, 15(1), 158. p. https://doi.org/10.1186/s13071-022-05260-4
  10. Fegraeus, K., Rosengren, M. K., Naboulsi, R., Orlando, L., Åbrink, M., Thorsell, A., Jouni, A., Velie, B. D., Raine, A., Egner, B., et al. (2022). An equine endothelin 3 cis-regulatory variant links blood pressure modulation to elite racing performance [Preprint]. bioRxiv, 2022–2011. pp. https://doi.org/10.1101/2022.11.04.515141
  11. Galmiche, M., Rodrigues, A., Motsch, E., Delhomme, O., Francois, Y.-N. and Millet, M. (2022). The use of pseudo-MRM for a sensitive and selective detection and quantification of polycyclic aromatic compounds by tandem mass spectrometry [Article]. Rapid Communications in Mass Spectrometry, 36(13). https://doi.org/10.1002/rcm.9307
  12. Ghadamgahi, F., Tarighi, S., Taheri, P., Saripella, G. V., Anzalone, A., Kalyandurg, P. B., Catara, V., Ortiz, R. and Vetukuri, R. R. (2022). Plant growth-promoting activity of pseudomonas aeruginosa FG106 and its ability to act as a biocontrol agent against potato, tomato and taro pathogens. Biology, 11(1), 140. p. https://doi.org/10.3390/biology11010140
  13. Grimberg, Å., Saripella, G. V., Repo-Carrasco Valencia, R. A.-M., Bengtsson, T., Alandia, G. and Carlsson, A. S. (2022). Transcriptional regulation of quinoa seed quality: Identification of novel candidate genetic markers for increased protein content. Frontiers in Plant Science, Volume 13 - 2022. https://doi.org/10.3389/fpls.2022.816425
  14. Hernández-Verdeja, T., Vuorijoki, L., Jin, X., Vergara, A., Dubreuil, C. and Strand, Å. (2022). GENOMES UNCOUPLED1 plays a key role during the de-etiolation process in arabidopsis. New Phytologist, 235(1), 188–203. pp. https://doi.org/10.1111/nph.18115
  15. Islam, M. M., Deepo, D. M., Nasif, S. O., Siddique, A. B., Hassan, O., Siddique, A. B. and Paul, N. C. (2022). Cytogenetics and consequences of polyploidization on different biotic-abiotic stress tolerance and the potential mechanisms involved. Plants, 11(20). https://doi.org/10.3390/plants11202684
  16. Jeilu, O., Simachew, A., Alexandersson, E., Johansson, E. and Gessesse, A. (2022). Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics [Article]. FRONTIERS IN MICROBIOLOGY, 13. https://doi.org/10.3389/fmicb.2022.1059061
  17. Karamat, F., Vergara, A., Blomberg, J., Crawford, T., Lehotai, N., Rentoft, M., Strand, Å. and Björklund, S. (2022). Arabidopsis mutants representing each of the four mediator modules reveal unique functions in the transcriptional response to salt stress [Preprint]. bioRxiv, 2022–2006. pp. https://doi.org/10.1101/2022.06.24.497547
  18. Law, S. R., Serrano, A. R., Daguerre, Y., Sundh, J., Schneider, A. N., Stangl, Z. R., Castro, D., Grabherr, M., Näsholm, T., Street, N. R., et al. (2022). Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. Proceedings of the National Academy of Sciences, 119(26), e2118852119. p. https://doi.org/10.1073/pnas.211885211
  19. Liebsch, D., Juvany, M., Li, Z., Wang, H.-L., Ziolkowska, A., Chrobok, D., Boussardon, C., Wen, X., Law, S. R., Janečková, H., et al. (2022). Metabolic control of arginine and ornithine levels paces the progression of leaf senescence. Plant Physiology, 189(4), 1943–1960. pp. https://doi.org/10.1093/plphys/kiac244
  20. Najafi, M., Guo, Y., Andersson, G., Humblot, P. and Bongcam-Rudloff, E. (2022). Gene networks and pathways involved in LPS-induced proliferative response of bovine endometrial epithelial cells. Genes, 13(12). https://doi.org/10.3390/genes13122342
  21. Öhlund, P., Delhomme, N., Hayer, J., Hesson, J. C. and Blomström, A.-L. (2022). Transcriptome analysis of an aedes albopictus cell line single-and dual-infected with lammi virus and WNV. International Journal of Molecular Sciences, 23(2), 875. p. https://doi.org/10.3390/ijms23020875
  22. Ranade, S. S., Seipel, G., Gorzsas, A. and Garcı́a-Gil, M. R. (2022). Adaptive strategies of scots pine under shade: Increase in lignin synthesis and ecotypic variation in defense-related gene expression. Physiologia Plantarum, 174(5), e13792. p. https://doi.org/10.1111/ppl.13792
  23. Ranade, S. S., Seipel, G., Gorzsás, A. and Garcı́a-Gil, M. R. (2022). Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in norway spruce. Plant, Cell & Environment, 45(9), 2671–2681. pp. https://doi.org/10.1111/pce.14387
  24. Ranjan, A., Perrone, I., Alallaq, S., Singh, R., Rigal, A., Brunoni, F., Chitarra, W., Guinet, F., Kohler, A., Martin, F., et al. (2022). Molecular basis of differential adventitious rooting competence in poplar genotypes. Journal of Experimental Botany, 73(12), 4046–4064. pp. https://doi.org/10.1093/jxb/erac126
  25. Siddique, A. B., Albrectsen, B. R., Ilbi, H. and Siddique, A. B. (2022). Optimization of protocol for construction of fungal ITS amplicon library for high-throughput illumina sequencing to study the mycobiome of aspen leaves. Applied Sciences, 12(3), 1136. p. https://doi.org/10.3390/app12031136
  26. Stenberg, H., Hellman, S., Lindstrom, L., Jacobson, M., Fossum, C., Hayer, J. and Malmberg, M. (2022). Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology [Article]. BMC VETERINARY RESEARCH, 18(1). https://doi.org/10.1186/s12917-022-03443-w
  27. Van Borm, S., Klingström, T. and Niazi, A. (2022). Host variation in susceptibility to lumpy skin disease: Gene expression analyses of experimentally infected cows. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 2022-07-03, Wageningen, the Netherlands. https://doi.org/10.3920/978-90-8686-940-4_154
  28. Veerkamp, R. and Haas, Y. de. (2022). Challenges–genetic control of infectious disease transmission and impact. Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 663–735. pp. https://doi.org/10.3920/9789086869404_153
  29. Vergara, A., Haas, J. C., Stachula, P., Street, N. R. and Hurry, V. (2022). Norway spruce deploys tissue-specific responses during acclimation to cold. Plant Cell Environ, 45, 427–445. pp. https://doi.org/10.1111/pce.14241
  30. Zacharaki, V., Ponnu, J., Crepin, N., Langenecker, T., Hagmann, J., Skorzinski, N., Musialak-Lange, M., Wahl, V., Rolland, F. and Schmid, M. (2022). Impaired KIN10 function restores developmental defects in the arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant. New Phytologist, 235(1), 220–233. pp. https://doi.org/10.1111/nph.18104

2021

  1. Azeez, A., Zhao, Y. C., Singh, R. K., Yordanov, Y. S., Dash, M., Miskolczi, P., Stojkovič, K., Strauss, S. H., Bhalerao, R. P. and Busov, V. B. (2021). EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy. Nature Communications, 12(1), 1123. p. https://doi.org/10.1038/s41467-021-21449-0
  2. Bag, P., Lihavainen, J., Delhomme, N., Riquelme, T., Robinson, K. M. and Jansson, S. (2021). An atlas of the norway spruce needle seasonal transcriptome. The Plant Journal, 108(6), 1815–1829. pp. https://doi.org/10.1111/tpj.15530
  3. Brouwer, S. M., Brus-Szkalej, M., Saripella, G. V., Liang, D., Liljeroth, E. and Grenville-Briggs, L. J. (2021). Transcriptome analysis of potato infected with the necrotrophic pathogen alternaria solani. Plants, 10(10), 2212. p. https://doi.org/10.3390/plants10102212
  4. Cabezas-Garcia, E. H., Danielsson, R., Ramin, M. and Huhtanen, P. (2021). In vitro incubations do not reflect in vivo differences based on ranking of low and high methane emitters in dairy cows. Animals, 11(11). https://doi.org/10.3390/ani11113112
  5. Christie, N., Mannapperuma, C., Ployet, R., Merwe, K. van der, Mähler, N., Delhomme, N., Naidoo, S., Mizrachi, E., Street, N. R. and Myburg, A. A. (2021). qtlXplorer: An online systems genetics browser in the eucalyptus genome integrative explorer (EucGenIE). BMC Bioinformatics, 22(1), 595. p. https://doi.org/10.1186/s12859-021-04514-9
  6. Cojkic, A., Niazi, A., Guo, Y., Hallap, T., Padrik, P. and Morrell, J. M. (2021). Identification of bull semen microbiome by 16S sequencing and possible relationships with fertility. Microorganisms, 9(12), 2431. p. https://doi.org/10.3390/microorganisms9122431
  7. Corduneanu, A., Mihalca, A. D., Sándor, A. D., Hornok, S., Malmberg, M., Viso, N. P. and Bongcam-Rudloff, E. (2021). The heart microbiome of insectivorous bats from central and south eastern europe. Comparative Immunology, Microbiology and Infectious Diseases, 75, 101605. p. https://doi.org/https://doi.org/10.1016/j.cimid.2020.101605
  8. Dobrenel, T., Kushwah, S., Mubeen, U., Jansen, W., Delhomme, N., Caldana, C. and Hanson, J. (2021). The phosphate starvation response recruits the TOR pathway to regulate growth in arabidopsis cell cultures. bioRxiv, 2021–2003. pp. https://doi.org/10.1101/2021.03.26.437164
  9. Friedrich, A., Bardhan, A., Maekawa, H., Schacherer, J., Knop, M., Delhomme, N., Dutreux, F., Papaioannou, I. A. and Peltier, F. (2021). Sex without crossing over in the yeast saccharomycodes ludwigii. Genome Biology, 22. https://doi.org/10.1186/s13059-021-02521-w
  10. Garnier, S., Harakalova, M., Weiss, S., Mokry, M., Regitz-Zagrosek, V., Hengstenberg, C., Cappola, T. P., Isnard, R., Arbustini, E., Cook, S. A., Setten, J. van, Calis, J. J. A., Hakonarson, H., Morley, M. P., Stark, K., Prasad, S. K., Li, J., O’Regan, D. P., Grasso, M., … Charron, G. consortium, Philippe. (2021). Genome-wide association analysis in dilated cardiomyopathy reveals two new players in systolic heart failure on chromosomes 3p25.1 and 22q11.23. European Heart Journal, 42(20), 2000–2011. pp. https://doi.org/10.1093/eurheartj/ehab030
  11. Haas, J. C., Vergara, A., Serrano, A. R., Mishra, S., Hurry, V. and Street, N. R. (2021). Candidate regulators and target genes of drought stress in needles and roots of norway spruce. Tree Physiology, 41(7), 1230–1246. pp. https://doi.org/10.1093/treephys/tpaa178
  12. Hayer, J., Wille, M., Font, A., González-Aravena, M., Norder, H. and Malmberg, M. (2021). Four novel picornaviruses detected in magellanic penguins (spheniscus magellanicus) in chile. Virology, 560, 116–123. pp. https://doi.org/10.1016/j.virol.2021.05.010
  13. Holmfeldt, K., Nilsson, E., Simone, D., Lopez-Fernandez, M., Wu, X., Bruijn, I. de, Lundin, D., Andersson, A. F., Bertilsson, S. and Dopson, M. (2021). The fennoscandian shield deep terrestrial virosphere suggests slow motion “boom and burst” cycles. Communications Biology, 4(1), 307. p. https://doi.org/10.1038/s42003-021-01810-1
  14. Juma, I., Geleta, M., Hovmalm, H. P., Nyomora, A., Saripella, G. V., Carlsson, A. S., Fatih, M. and Ortiz, R. (2021). Comparison of morphological and genetic characteristics of avocados grown in tanzania. Genes, 12(1). https://doi.org/10.3390/genes12010063
  15. Kahlert, M., Bailet, B., Chonova, T., Karjalainen, S. M., Schneider, S. C. and Tapolczai, K. (2021). Same same, but different: The response of diatoms to environmental gradients in fennoscandian streams and lakes – barcodes, traits and microscope data compared. Ecological Indicators, 130, 108088. p. https://doi.org//10.1016/j.ecolind.2021.108088
  16. Lihavainen, J., Edlund, E., Björkén, L., Bag, P., Robinson, K. M. and Jansson, S. (2021). Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals. Physiologia Plantarum, 172(1), 201–217. pp. https://doi.org/10.1111/ppl.13319
  17. Liu, H., Yan, X.-M., Wang, X., Zhang, D.-X., Zhou, Q., Shi, T.-L., Jia, K.-H., Tian, X.-C., Zhou, S.-S., Zhang, R.-G., et al. (2021). Centromere-specific retrotransposons and very-long-chain fatty acid biosynthesis in the genome of yellowhorn (xanthoceras sorbifolium, sapindaceae), an oil-producing tree with significant drought resistance. Frontiers in Plant Science, 12, 766389. p. https://doi.org/10.3389/fpls.2021.766389
  18. Mahboubi, A., Delhomme, N., Häggström, S. and Hanson, J. (2021). Small-scale sequencing enables quality assessment of ribo-seq data: An example from arabidopsis cell culture. Plant Methods, 17(1), 92. p. https://doi.org/10.1186/s13007-021-00791-w
  19. Mahmud, A. F., Delhomme, N., Nandi, S. and Fällman, M. (2021). ProkSeq for complete analysis of RNA-seq data from prokaryotes. Bioinformatics, 37(1), 126–128. pp. https://doi.org/10.1093/bioinformatics/btaa1063
  20. Martin, F., Halvarsson, P., Delhomme, N., Höglund, J. and Tyden, E. (2021). Exploring the \(\beta\)-tubulin gene family in a benzimidazole-resistant parascaris univalens population. International Journal for Parasitology: Drugs and Drug Resistance, 17, 84–91. pp. https://doi.org/10.1016/j.ijpddr.2021.08.004
  21. Mehrshad, M., Lopez-Fernandez, M., Sundh, J., Bell, E., Simone, D., Buck, M., Bernier-Latmani, R., Bertilsson, S. and Dopson, M. (2021). Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nature Communications, 12(1), 4253. p. https://doi.org/10.1038/s41467-021-24549-z
  22. Mishra, L. S., Mishra, S., Caddell, D. F., Coleman-Derr, D. and Funk, C. (2021). The plastid-localized AtFtsHi3 pseudo-protease of arabidopsis thaliana has an impact on plant growth and drought tolerance. Frontiers in Plant Science, 12, 694727. p. https://doi.org/10.3389/fpls.2021.694727
  23. Moestedt, J., Westerholm, M., Isaksson, S. and Schnurer, A. (2021). Production during anaerobic digestion of sewage sludge and food waste. Current Advances in Anaerobic Digestion Technology, 153. p. https://mdpi-res.com/bookfiles/book/3502/Current_Advances_in_Anaerobic_Digestion_Technology.pdf
  24. Morange, P.-E., Peiretti, F., Gourhant, L., Proust, C., Soukarieh, O., Pulcrano-Nicolas, A.-S., Saripella, G.-V., Stefanucci, L., Lacroix, R., Ibrahim-Kosta, M., et al. (2021). A rare coding mutation in the MAST2 gene causes venous thrombosis in a french family with unexplained thrombophilia: The breizh MAST2 Arg89Gln variant. PLoS Genetics, 17(1), e1009284. p. https://doi.org/10.1371/journal.pgen.1009284
  25. Ranade, S. S. and Garcı́a-Gil, M. R. (2021). Molecular signatures of local adaptation to light in norway spruce. Planta, 253(2), 53. p. https://doi.org/10.1007/s00425-020-03517-9
  26. Schneider, A. N., Sundh, J., Sundström, G., Richau, K., Delhomme, N., Grabherr, M., Hurry, V. and Street, N. R. (2021). Comparative fungal community analyses using metatranscriptomics and internal transcribed spacer amplicon sequencing from norway spruce. Msystems, 6(1), 10–1128. pp. https://doi.org/10.1128/msystems.00884-20
  27. Seyfferth, C., Wessels, B. A., Vahala, J., Kangasjärvi, J., Delhomme, N., Hvidsten, T. R., Tuominen, H. and Lundberg-Felten, J. (2021). Populus PtERF85 balances xylem cell expansion and secondary cell wall formation in hybrid aspen. Cells, 10(8). https://doi.org/10.3390/cells10081971
  28. Van Damme, R., Hölzer, M., Viehweger, A., Müller, B., Bongcam–Rudloff, E. and Brandt, C. (2021). Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PLOS Computational Biology, 17(2), e1008716. p. https://doi.org/10.1371/journal.pcbi.1008716

2020

  1. Al-Kass, Z., Guo, Y., Vinnere Pettersson, O., Niazi, A. and Morrell, J. M. (2020). Metagenomic analysis of bacteria in stallion semen. Animal Reproduction Science, 221, 106568. p. https://doi.org/10.1016/j.anireprosci.2020.106568
  2. Brunoni, F., Collani, S., Casanova-Sáez, R., Šimura, J., Karady, M., Schmid, M., Ljung, K. and Bellini, C. (2020). Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis. New Phytologist, 226(6), 1753–1765. pp. https://doi.org/10.1111/nph.16463
  3. Crawford, T., Karamat, F., Lehotai, N., Rentoft, M., Blomberg, J., Strand, Å. and Björklund, S. (2020). Specific functions for mediator complex subunits from different modules in the transcriptional response of arabidopsis thaliana to abiotic stress. Scientific Reports, 10(1), 5073. p. https://doi.org/10.1038/s41598-020-61758-w
  4. Frosth, S., Karlsson-Lindsjö, O., Niazi, A., Fernström, L.-L. and Hansson, I. (2020). Identification of transmission routes of campylobacter and on-farm measures to reduce campylobacter in chicken. Pathogens, 9(5), 363. p. https://doi.org/10.3390/pathogens9050363
  5. Gil-Muñoz, F., Delhomme, N., Quiñones, A., Naval, M. del M., Badenes, M. L. and Garcı́a-Gil, M. R. (2020). Transcriptomic analysis reveals salt tolerance mechanisms present in date-plum persimmon rootstock (diospyros lotus l.). Agronomy, 10(11), 1703. p. https://doi.org/10.3390/agronomy10111703
  6. Hammenhag, C., Saripella, G. V., Ortiz, R. and Geleta, M. (2020). QTL mapping for domestication-related characteristics in field cress (lepidium campestre)—a novel oil crop for the subarctic region. Genes, 11(10), 1223. p. 10.3390/genes11101223
  7. Jhamat, N., Niazi, A., Guo, Y., Chanrot, M., Ivanova, E., Kelsey, G., Bongcam-Rudloff, E., Andersson, G. and Humblot, P. (2020). LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function. BMC Genomics, 21(1), 385. p. https://doi.org/10.1186/s12864-020-06777-7
  8. Kumar, V., Donev, E. N., Barbut, F. R., Kushwah, S., Mannapperuma, C., Urbancsok, J. and Mellerowicz, E. J. (2020). Genome-wide identification of populus malectin/malectin-like domain-containing proteins and expression analyses reveal novel candidates for signaling and regulation of wood development. Frontiers in Plant Science, 11, 588846. p. https://doi.org/10.3389/fpls.2020.588846
  9. Lakehal, A., Dob, A., Rahneshan, Z., Novák, O., Escamez, S., Alallaq, S., Strnad, M., Tuominen, H. and Bellini, C. (2020). ETHYLENE RESPONSE FACTOR 115 integrates jasmonate and cytokinin signaling machineries to repress adventitious rooting in arabidopsis. New Phytologist, 228(5), 1611–1626. pp. https://doi.org/10.1111/nph.16794
  10. Lecoy, J. and Garciá-Gil, M. (2020). Evolutionary analysis of LP3 gene family in conifers: An ASR homolog. bioRxiv, 2020–2003. pp. https://doi.org/10.1101/2020.03.27.011197
  11. Mannapperuma, C., Liu, H., Bel, M., Delhomme, N., Serrano, A., Schiffthaler, B., Hvidsten, T. R., Vandepoele, K., Ayllón-Benı́tez, A. and Street, N. (2020). Plantgenie-plaza: Integrating orthology into the plantgenie. Org resource using the plaza pipeline [Preprint]. Umeå Universitet, Diva Portal.
  12. Martin, F., Dube, F., Karlsson Lindsjö, O., Eydal, M., Höglund, J., Bergström, T. F. and Tydén, E. (2020). Transcriptional responses in parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole. Parasites & Vectors, 13(1), 342. p. https://doi.org/0.1186/s13071-020-04212-0
  13. Moestedt, J., Müller, B., Nagavara Nagaraj, Y. and Schnürer, A. (2020). Acetate and lactate production during two-stage anaerobic digestion of food waste driven by lactobacillus and aeriscardovia. Frontiers in Energy Research, 8, 105. p. https://doi.org/10.3389/fenrg.2020.00105
  14. Moestedt, J., Westerholm, M., Isaksson, S. and Schnürer, A. (2020). Inoculum source determines acetate and lactate production during anaerobic digestion of sewage sludge and food waste. Bioengineering, 7(1). https://doi.org/10.3390/bioengineering7010003
  15. Obi, I., Rentoft, M., Singh, V., Jamroskovic, J., Chand, K., Chorell, E., Westerlund, F. and Sabouri, N. (2020). Stabilization of g-quadruplex DNA structures in schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication. Nucleic Acids Research, 48(19), 10998–11015. pp. https://doi.org/10.1093/nar/gkaa820
  16. Peura, S., Wauthy, M., Simone, D., Eiler, A., Einarsdottir, K., Rautio, M. and Bertilsson, S. (2020). Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential [Article]. LIMNOLOGY AND OCEANOGRAPHY, 65(1, SI), S248–S263. pp. https://doi.org/10.1002/lno.11349
  17. Peura, S., Wauthy, M., Simone, D., Eiler, A., Einarsdóttir, K., Rautio, M. and Bertilsson, S. (2020). Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential. Limnology and Oceanography, 65(S1), S248–S263. pp. https://doi.org/10.1002/lno.11349
  18. Senanayake, K. S., Söderberg, J., Polajev, A., Malmberg, M., Karunanayake, E. H., Tennekoon, K. H., Samarakoon, S. R., Bongcam-Rudloff, E. and Niazi, A. (2020). The genome of setaria digitata: A cattle nematode closely related to human filarial parasites. Genome Biology and Evolution, 12(2), 3971–3976. pp. https://doi.org/10.1093/gbe/evaa017
  19. Sullivan, A. R., Eldfjell, Y., Schiffthaler, B., Delhomme, N., Asp, T., Hebelstrup, K. H., Keech, O., Öberg, L., Møller, I. M., Arvestad, L., et al. (2020). The mitogenome of norway spruce and a reappraisal of mitochondrial recombination in plants. Genome Biology and Evolution, 12(1), 3586–3598. pp. https://doi.org/10.1093/gbe/evz263
  20. Wille, M., Wensman, J. J., Larsson, S., van Damme, R., Theelke, A.-K., Hayer, J. and Malmberg, M. (2020). Evolutionary genetics of canine respiratory coronavirus and recent introduction into swedish dogs. Infection, Genetics and Evolution, 82, 104290. p. https://doi.org/https://doi.org/10.1016/j.meegid.2020.104290
  21. Zhang, B., Sztojka, B., Seyfferth, C., Escamez, S., Miskolczi, P., Chantreau, M., Bakó, L., Delhomme, N., Gorzsás, A., Bhalerao, R. P., et al. (2020). The chromatin-modifying protein HUB2 is involved in the regulation of lignin composition in xylem vessels. Journal of Experimental Botany, 71(18), 5484–5494. pp. https://doi.org/10.1093/jxb/eraa264

2019

  1. Bai, B., Horst, S. van der, Delhomme, N., Robles, A. V., Bentsink, L. and Hanson, J. (2019). Transcriptome and translatome profiling and translational network analysis during seed maturation reveals conserved transcriptional and distinct translational regulatory patterns. bioRxiv, 778001. p. https://doi.org/10.1101/778001
  2. Blokhina, O., Laitinen, T., Hatakeyama, Y., Delhomme, N., Paasela, T., Zhao, L., Street, N. R., Wada, H., Kärkönen, A. and Fagerstedt, K. (2019). Ray parenchymal cells contribute to lignification of tracheids in developing xylem of norway spruce. Plant Physiology, 181(4), 1552–1572. pp. https://doi.org/10.1104/pp.19.00743
  3. Collani, S., Neumann, M., Yant, L. and Schmid, M. (2019). FT modulates genome-wide DNA-binding of the bZIP transcription factor FD. Plant Physiology, 180(1), 367–380. pp. https://doi.org/10.1104/pp.18.01505
  4. Dahlberg, J., Sun, L., Waller, K. P., Ostensson, K., McGuire, M., Agenas, S. and Dicksved, J. (2019). Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination [Article]. PLoS One, 14(6). https://doi.org/10.1371/journal.pone.0218257
  5. Giacomello, S., Delhomme, N., Niittyla, T., Tuominen, H. and Street, N. R. (2019). High spatial resolution profiling in tree species [Article]. Annual Plant Reviews Online, 2(1), 329–359. pp. https://doi.org/10.1002/9781119312994.apr0688
  6. Gourle, H., Karlsson-Lindsjo, O., Hayer, J. and Bongcam-Rudloff, E. (2019). Simulating illumina metagenomic data with InSilicoSeq [Article]. Bioinformatics, 35(3), 521–522. pp. https://doi.org/10.1093/bioinformatics/bty630
  7. Guo, Y., Schaik, T. van, Jhamat, N., Niazi, A., Chanrot, M., Charpigny, G., Valarcher, J. F., Bongcam-Rudloff, E., Andersson, G. and Humblot, P. (2019). Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions [Article]. PLoS One, 14(9). https://doi.org/10.1371/journal.pone.0222081
  8. Kloth, K. J., Abreu, I. N., Delhomme, N., Petrik, I., Villard, C., Strom, C., Amini, F., Novak, O., Moritz, T. and Albrectsen, B. R. (2019). PECTIN ACETYLESTERASE9 affects the transcriptome and metabolome and delays aphid Feeding1[OPEN] [Article]. Plant Physiology, 181(4), 1704–1720. pp. https://doi.org/10.1104/pp.19.00635
  9. Kumar, V., Hainaut, M., Delhomme, N., Mannapperuma, C., Immerzeel, P., Street, N. R., Henrissat, B. and Mellerowicz, E. J. (2019). Poplar carbohydrate-active enzymes: Whole-genome annotation and functional analyses based on RNA expression data [Article]. Plant Journal, 99(4), 589–609. pp. https://doi.org/10.1111/tpj.14417
  10. Lopez-Fernandez, M., Broman, E., Simone, D., Bertilsson, S. and Dopson, M. (2019). Statistical analysis of community RNA transcripts between organic carbon and geogas-fed continental deep biosphere groundwaters [Article]. MBIO, 10(4). https://doi.org/10.1128/mBio.01470-19
  11. Mannapperuma, C., Street, N. and Waterworth, J. (2019). Designing usable bioinformatics tools for specialized users. International Conference on Information Technology & Systems, 649–670. pp. https://doi.org/10.1007/978-3-030-11890-7_62
  12. Mannapperuma, C., Waterworth, J. and Street, N. (2019). GenIE-sys: Genome integrative explorer system. bioRxiv, 808881. p. https://doi.org/10.1101/808881
  13. Odilbekov, F., Armoniene, R., Koc, A., Svensson, J. and Chawade, A. (2019). GWAS-assisted genomic prediction to predict resistance to septoria tritici blotch in nordic winter wheat at seedling stage [Article]. FRONTIERS IN GENETICS, 10. https://doi.org/10.3389/fgene.2019.01224
  14. Odilbekov, F., He, X., Armoniene, R., Saripella, G. V., Henriksson, T., Singh, P. K. and Chawade, A. (2019). QTL mapping and transcriptome analysis to identify differentially expressed genes induced by septoria tritici blotch disease of wheat [Article]. Agronomy-Basel, 9(9). https://doi.org/10.3390/agronomy9090510
  15. Ohlund, P., Hayer, J., Lunden, H., Hesson, J. C. and Blomstrom, A.-L. (2019). Viromics reveal a number of novel RNA viruses in swedish mosquitoes [Article]. Viruses, 11(11). https://doi.org/10.3390/v11111027
  16. Ranade, S. S., Delhomme, N. and Garcia-Gil, M. R. (2019a). Global gene expression analysis in etiolated and de-etiolated seedlings in conifers [Article]. PLoS One, 14(7). https://doi.org/10.1371/journal.pone.0219272
  17. Ranade, S. S., Delhomme, N. and Garcia-Gil, M. R. (2019b). Transcriptome analysis of shade avoidance and shade tolerance in conifers [Article]. PLANTA, 250(1), 299–318. pp. https://doi.org/10.1007/s00425-019-03160-z
  18. Schiffthaler, B., Serrano, A., Street, N. and Delhomme, N. (2019). Seiðr: A gene meta-network calculation toolkit. bioRxiv, 4, 250696. p.
  19. Seyfferth, C., Wessels, B. A., Gorzsas, A., Love, J. W., Ruggeberg, M., Delhomme, N., Vain, T., Antos, K., Tuominen, H., Sundberg, B. and Felten, J. (2019). Ethylene signaling is required for fully functional tension wood in hybrid aspen [Article]. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.01101
  20. Singh, A., Mueller, B., Fuxelius, H.-H. and Schnurer, A. (2019). AcetoBase: A functional gene repository and database for formyltetrahydrofolate synthetase sequences [Article]. Database. https://doi.org/10.1093/database/baz142
  21. Vain, T., Raggi, S., Ferro, N., Barange, D. K., Kieffer, M., Ma, Q., Doyle, S. M., Thelander, M., Parizkova, B., Novak, O., Ismail, A., Enquist, P.-A., Rigal, A., Langowska, M., Harborough, S. R., Zhang, Y., Ljung, K., Callis, J., Almqvist, F., … Robert, S. (2019). Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development [Article]. Proceedings of the National Academy of Sciences, 116(13), 6463–6472. pp. https://doi.org/10.1073/pnas.1809037116
  22. Wessels, B., Seyfferth, C., Escamez, S., Vain, T., Antos, K., Vahala, J., Delhomme, N., Kangasjarvi, J., Eder, M., Felten, J. and Tuominen, H. (2019). An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition [Article]. New Phytologist, 224(4), 1585–1599. pp. https://doi.org/10.1111/nph.15960

2018

  1. Akhter, S., Kretzschmar, W. W., Nordal, V., Delhomme, N., Street, N. R., Nilsson, O., Emanuelsson, O. and Sundstrom, J. F. (2018). Integrative analysis of three RNA sequencing methods identifies mutually exclusive exons of MADS-box isoforms during early bud development in picea abies [Article]. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.01625
  2. Capovilla, G., Delhomme, N., Collani, S., Shutava, I., Bezrukov, I., Symeonidi, E., Amorim, M. de F., Laubinger, S. and Schmid, M. (2018). PORCUPINE regulates development in response to temperature through alternative splicing [Article]. Nature Plants, 4(8), 534–539. pp. https://doi.org/10.1038/s41477-018-0176-z
  3. Cholleti, H., Hayer, J., Fafetine, J., Berg, M. and Blomstrom, A.-L. (2018). Genetic characterization of a novel picorna-like virus in &ITCulex&IT spp. Mosquitoes from mozambique [Article]. Virology Journal, 15. https://doi.org/10.1186/s12985-018-0981-z
  4. Collani, S., Neumann, M., Yant, L. and Schmid, M. (2018). Effects of FLOWERING LOCUS t on FD during the transition to flowering at the shoot apical meristem of arabidopsis thaliana. bioRxiv, 483925. p. https://doi.org/10.1101/483925
  5. Delhomme, F., Pallud, B. and Rouane, N. (2018). Tightening torque influence on pullout behavior of post-installed expansion anchors [Article]. KSCE Journal of Civil Engineering, 22(10), 3931–3939. pp. https://doi.org/10.1007/s12205-018-0930-9
  6. Felten, J., Vahala, J., Love, J., Gorzsas, A., Ruggeberg, M., Delhomme, N., Lesniewska, J., Kangasjarvi, J., Hvidsten, T. R., Mellerowicz, E. J. and Sundberg, B. (2018). Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen [Article]. New Phytologist, 218(3, SI), 999–1014. pp. https://doi.org/10.1111/nph.15078
  7. Ferro, L., Gentili, F. G. and Funk, C. (2018). Isolation and characterization of microalgal strains for biomass production and wastewater reclamation in northern sweden [Article]. Algal Research, 32, 44–53. pp. https://doi.org/10.1016/j.algal.2018.03.006
  8. Jenjaroenpun, P., Wongsurawat, T., Pereira, R., Patumcharoenpol, P., Ussery, D. W., Nielsen, J. and Nookaew, I. (2018). Complete genomic and transcriptional landscape analysis using third-generation sequencing: A case study of saccharomyces cerevisiae CEN. PK113-7D. Nucleic Acids Research, 46(7), e38–e38. pp. https://doi.org/10.1093/nar/gky014
  9. Jokipii-Lukkari, S., Delhomme, N., Schiffthaler, B., Mannapperuma, C., Prestele, J., Nilsson, O., Street, N. R. and Tuominen, H. (2018). Transcriptional roadmap to seasonal variation in wood formation of norway spruce [Article]. Plant Physiology, 176(4), 2851–2870. pp. https://doi.org/10.1104/pp.17.01590
  10. L Pourbozorgi, P., Delhomme, N., Obi, I., Mohammad, J. B. and Sabouri, N. (2018). Topoisomerase 1 and the Pfh1 helicase are both required for proper DNA synthesis [Preprint]. Diva, Umeå University.
  11. L Pourbozorgi, P., Delhomme, N., Obi, I. and Sabouri, N. (2018). Top1 and Pfh1Pif1 maintain the s. Pombe mitochondrial genome [Preprint]. Diva, Umeå University.
  12. Law, S. R., Chrobok, D., Juvany, M., Delhomme, N., Linden, P., Brouwer, B., Ahad, A., Moritz, T., Jansson, S., Gardestrom, P. and Keech, O. (2018). Darkened leaves use different metabolic strategies for senescence and survival [Article]. Plant Physiology, 177(1), 132–150. pp. https://doi.org/10.1104/pp.18.00062
  13. Leblay, N., Alcala, N., Marin, D. H., Delhomme, T. M., Giffon, T., Ghantous, A., Chabrier, A., Cuenin, C., Altmueller, J., Durand, G., Voegele, C., Lorimier, P., Toffart, A.-C., Derks, J., Brustugun, O. T., Clement, J. H., Saenger, J., Field, J. K., Soltermann, A., … Fernandez-Cuesta, L. (2018). Multi-omics comparative analyses of pulmonary typical carcinoids, atypical carcinoids, and large-cell neuroendocrine carcinoma [Meeting Abstract]. Cancer Research, 78(13, S). https://doi.org/10.1158/1538-7445.AM2018-5358
  14. Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundstrom, G., Zuccolo, A., Nystedt, B., Hvidsten, T. R., Torre, A. de la, Cossu, R. M., Hoeppner, M. P., Lantz, H., Scofield, D. G., Zamani, N., Johansson, A., Mannapperuma, C., Robinson, K. M., Mahler, N., Leitch, I. J., … Street, N. R. (2018). Functional and evolutionary genomic inferences in populus through genome and population sequencing of american and european aspen [Article]. Proceedings of the National Academy of Sciences of the United States of America, 115(46), E10970–E10978. pp. https://doi.org/10.1073/pnas.1801437115
  15. Manzoor, S., Schnurer, A., Bongcam-Rudloff, E. and Muller, B. (2018). Genome-guided analysis of clostridium ultunense and comparative genomics reveal different strategies for acetate oxidation and energy conservation in syntrophic acetate-oxidising bacteria [Article]. Genes, 9(4). https://doi.org/10.3390/genes9040225
  16. Reza, S. H., Delhomme, N., Street, N. R., Ramachandran, P., Dalman, K., Nilsson, O., Minina, E. A. and Bozhkov, P. V. (2018). Transcriptome analysis of embryonic domains in norway spruce reveals potential regulators of suspensor cell death [Article]. PLoS One, 13(3). https://doi.org/10.1371/journal.pone.0192945
  17. Seyfferth, C., Wessels, B., Jokipii-Lukkari, S., Sundberg, B., Delhomme, N., Felten, J. and Tuominen, H. (2018). Ethylene-related gene expression networks in wood formation [Article]. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.00272
  18. Singh, R. K., Maurya, J. P., Azeez, A., Miskolczi, P., Tylewicz, S., Stojkovic, K., Delhomme, N., Busov, V. and Bhalerao, R. P. (2018). A genetic network mediating the control of bud break in hybrid aspen [Article]. Nature Communications, 9. https://doi.org/10.1038/s41467-018-06696-y
  19. Sundström, G., Schneider, A. N., Richau, K., Haas, J. C., Delhomme, N., Sjödin, A., Hurry, V., Grabherr, M. and Street, N. R. (2018). Reproducibility and biological information of tree-associated metacommunities using RNA sequencing and DNA amplicon profiling. Diva. https://www.diva-portal.org/smash/record.jsf?pid=diva2%3A1259386&dswid=-7962
  20. Zare, A., Johansson, A.-M., Karlsson, E., Delhomme, N. and Stenberg, P. (2018). The gut microbiome participates in transgenerational inheritance of low-temperature responses in drosophila melanogaster [Article]. Febs Letters, 592(24), 4078–4086. pp. https://doi.org/10.1002/1873-3468.13278