BILS publications

2016

Abrouk, M., Balcárková, B., Šimková, H., Komı́nkova Eva, Martis, M. M., Jakobson, I., Timofejeva, L., Rey, E., Vrána, J., Kilian, A., Järve, K., Doležel, J., and Valárik, M. (2016) Thein silicoidentification and characterization of a bread wheat/Triticum militinaeintrogression line. Plant Biotechnology Journal.

Alvarsson, J., Lampa, S., Schaal, W., Andersson, C., Wikberg, J. E. S., and Spjuth, O. (2016) Large-scale ligand-based predictive modelling using support vector machines. Journal of Cheminformatics, 8.

Astakhova, L., Ngara, M., Babich, O., Prosekov, A., Asyakina, L., Dyshlyuk, L., Midtvedt, T., Zhou, X., Ernberg, I., and Matskova, L. (2016) Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells. PLOS ONE, 11, e0154102.

Bagnoud, A., Chourey, K., Hettich, R. L., Bruijn, I. de, Andersson, A. F., Leupin, O. X., Schwyn, B., and Bernier-Latmani, R. (2016) Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock. Nature Communications, 7, 12770.

Barrio, A. M. et al. (2016) The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLife, 5.

Bauer, E., Schmutzer, T., Barilar, I., Mascher, M., Gundlach, H., Martis, M. M., Twardziok, S. O., Hackauf, B., Gordillo, A., Wilde, P., Schmidt, M., Korzun, V., Mayer, K. F. X., Schmid, K., Schön, C.-C., and Scholz, U. (2016) Towards a whole-genome sequence for rye ( Secale cereale L.) . The Plant Journal.

Berglund, U. W. et al. (2016) Validation and development of MTH1 inhibitors for treatment of cancer. Annals of Oncology, mdw429.

Buetti-Dinh, A., Dethlefsen, O., Friedman, R., and Dopson, M. (2016) Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes. Microbiology (Reading, Engl.), 162, 1422–1434.

Chawade, A., Alexandersson, E., Bengtsson, T., Andreasson, E., and Levander, F. (2016) Targeted Proteomics Approach for Precision Plant Breeding. Journal of Proteome Research, 15, 638–646.

Christel, S., Fridlund, J., Buetti-Dinh, A., Buck, M., Watkin, E. L., and Dopson, M. (2016) RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans . FEMS Microbiology Letters, 363, fnw057.

Diez, B., Nylander, J. A., Ininbergs, K., Dupont, C. L., Allen, A. E., Yooseph, S., Rusch, D. B., and Bergman, B. (2016) Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution. PLoS ONE, 11, e0155757.

Engel, P. et al. (2016) The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions. mBio, 7, e02164–15.

Engström, K., Wojdacz, T. K., Marabita, F., Ewels, P., Käller, M., Vezzi, F., Prezza, N., Gruselius, J., Vahter, M., and Broberg, K. (2016) Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women. Archives of Toxicology.

Fernandez-Ricaud, L., Kourtchenko, O., Zackrisson, M., Warringer, J., and Blomberg, A. (2016) PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics. BMC Bioinformatics, 17, 249.

Hall, U. A., Edin, F., Pedersen, A., and Madsen, K. (2016) Whole-body fat oxidation increases more by prior exercise than overnight fasting in elite endurance athletes. Appl. Physiol. Nutr. Metab., 41, 430–437.

Hambäck, P. A., Weingartner, E., Dalén, L., Wirta, H., and Roslin, T. (2016) Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes. Ecology and Evolution.

Hayat, S., Peters, C., Shu, N., Tsirigos, K. D., and Elofsson, A. (2016) Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins. Bioinformatics, 32, 1571–1573.

Huang, Y., Chain, F. J. J., Panchal, M., Eizaguirre, C., Kalbe, M., Lenz, T. L., Samonte, I. E., Stoll, M., Bornberg-Bauer, E., Reusch, T. B. H., Milinski, M., and Feulner, P. G. D. (2016) Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Molecular Ecology, 25, 943–958.

Husa, A. M., MagiA, A. E., Larsson, M., Fornander, T., and Perez-Tenorio, G. (2016) EPH/ephrin profile and EPHB2 expression predicts patient survival in breast cancer. Oncotarget, .

Jonsson, K., Barman, M., Moberg, S., Sjoberg, A., Brekke, H. K., Hesselmar, B., Johansen, S., Wold, A. E., and Sandberg, A. S. (2016) Fat intake and breast milk fatty acid composition in farming and nonfarming women and allergy development in the offspring. Pediatr. Res., 79, 114–123.

Kalanxhi, E., Risberg, K., Barua, I. S., Dueland, S., Waagene, S., Andersen, S. N., Pettersen, S. J., Lindvall, J. M., Redalen, K. R., Flatmark, K., and Ree, A. H. (2016) Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy. Cancer Research and Treatment.

Karimpour, M., Surowiec, I., Wu, J., Gouveia-Figueira, S., Pinto, R., Trygg, J., Zivkovic, A. M., and Nording, M. L. (2016) Postprandial metabolomics: A pilot mass spectrometry and NMR study of the human plasma metabolome in response to a challenge meal. Analytica Chimica Acta, 908, 121–131.

Kirchner, H., Sinha, I., Gao, H., Ruby, M. A., Schönke, M., Lindvall, J. M., Barrès, R., Krook, A., Näslund, E., Dahlman-Wright, K., and Zierath, J. R. (2016) Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients. Molecular Metabolism, 5, 171–183.

Lampa, S., Alvarsson, J., and Spjuth, O. (2016) Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles. Journal of Cheminformatics, 8.

Landegren, N., Sharon, D., Freyhult, E., Hallgren, Åsa, Eriksson, D., Edqvist, P.-H., Bensing, S., Wahlberg, J., Nelson, L. M., Gustafsson, J., Husebye, E. S., Anderson, M. S., Snyder, M., and Kämpe, O. (2016) Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1. Sci. Rep., 6, 20104.

Levin, M., Levander, F., Palmason, R., Greiff, L., and Ohlin, M. (2016) Antibody-encoding repertoires of bone marrow and peripheral blood—a focus on IgE. Journal of Allergy and Clinical Immunology.

Li, X., Padhan, N., Sjöström, E. O., Roche, F. P., Testini, C., Honkura, N., Sáinz-Jaspeado, M., Gordon, E., Bentley, K., Philippides, A., Tolmachev, V., Dejana, E., Stan, R. V., Vestweber, D., Ballmer-Hofer, K., Betsholtz, C., Pietras, K., Jansson, L., and Claesson-Welsh, L. (2016) VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread. Nature Communications, 7, 11017.

Lind, A.-L., Wu, D., Freyhult, E., Bodolea, C., Ekegren, T., Larsson, A., Gustafsson, M. G., Katila, L., Bergquist, J., Gordh, T., Landegren, U., and Kamali-Moghaddam, M. (2016) A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients. PLOS ONE, 11, e0149821.

Lindblad, O., Cordero, E., Puissant, A., Macaulay, L., Ramos, A., Kabir, N. N., Sun, J., Vallon-Christersson, J., Haraldsson, K., Hemann, M. T., Borg, Å., Levander, F., Stegmaier, K., Pietras, K., Rönnstrand, L., and Kazi, J. U. (2016) Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML. Oncogene, 35, 5119–5131.

Lindqvist, C. M., Lundmark, A., Nordlund, J., Freyhult, E., Ekman, D., Almlof, J. C., Raine, A., Overnas, E., Abrahamsson, J., Frost, B. M., Grander, D., Heyman, M., Palle, J., Forestier, E., Lonnerholm, G., Berglund, E. C., and Syvanen, A. C. (2016) Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. Oncotarget.

Ma, W., Gabriel, T. S., Martis, M. M., Gursinsky, T., Schubert, V., Vrána, J., Doležel, J., Grundlach, H., Altschmied, L., Scholz, U., Himmelbach, A., Behrens, S.-E., Banaei-Moghaddam, A. M., and Houben, A. (2016) Rye B chromosomes encode a functional Argonaute-like protein within~vitroslicer activities similar to its A chromosome paralog. New Phytologist.

Ma, W., Schubert, V., Martis, M. M., Hause, G., Liu, Z., Shen, Y., Conrad, U., Shi, W., Scholz, U., Taudien, S., Cheng, Z., and Houben, A. (2016) The distribution of α-kleisin during meiosis in the holocentromeric plant Luzula elegans. Chromosome Research, 24, 393–405.

Marabita, F. and Islam, M. S. (2016) Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic β-Cells. Pancreas, 1.

Martı́nez-Redondo Vicente, Jannig, P. R., Correia, J. C., Ferreira, D. M. S., Cervenka, I., Lindvall, J. M., Sinha, I., Izadi, M., Pettersson-Klein, A. T., Agudelo, L. Z., Gimenez-Cassina, A., Brum, P. C., Dahlman-Wright, K., and Ruas, J. L. (2016) Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes. Journal of Biological Chemistry, 291, 15169–15184.

Mendoza, M. L. Z., Lundberg, J., Ivarsson, M., Campos, P., Nylander, J. A. A., Sallstedt, T., and Dalen, L. (2016) Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante’s Cave, Northern Sweden. PLOS ONE, 11, e0151577.

Moghadam, B. T., Dabrowski, M., Kaminska, B., Grabherr, M. G., and Komorowski, J. (2016) Combinatorial identification of DNA methylation patterns over age in the human brain. BMC Bioinformatics, 17.

Mukwaya, A., Lindvall, J. M., Xeroudaki, M., Peebo, B., Ali, Z., Lennikov, A., Jensen, L. D. E., and Lagali, N. (2016) A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis. Scientific Data, 3, 160103.

Nilsson, R. H., Rosenblad, M. A., Martı́n Marı́a P., Tedersoo, L., Ryberg, M. K., Larsson, E., Wurzbacher, C., and Abarenkov, K. (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys, 13, 21–33.

Norling, M., Karlsson-Lindsjö, O. E., Gourlé, H., Bongcam-Rudloff, E., and Hayer, J. (2016) MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies. PLOS ONE, 11, e0160334.

Obudulu, O., Bygdell, J., Sundberg, B., Moritz, T., Hvidsten, T. R., Trygg, J., and Wingsle, G. (2016) Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. BMC Genomics, 17.

Olsen, J. L. et al. (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature, 530, 331–335.

Pauter, A. M., Trattner, S., Gonzalez-Bengtsson, A., Talamonti, E., Asadi, A., Dethlefsen, O., and Jacobsson, A. (2016) Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice. Journal of Lipid Research, jlr.M070862.

Persson, J., Steglich, B., Smialowska, A., Boyd, M., Bornholdt, J., Andersson, R., Schurra, C., Arcangioli, B., Sandelin, A., Nielsen, O., and Ekwall, K. (2016) Regulating retrotransposon activity through the use of alternative transcription start sites. EMBO Rep., 17, 753–768.

Peters, C., Tsirigos, K. D., Shu, N., and Elofsson, A. (2016) Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics, 32, 1158–1162.

Ryden, M., Hrydziuszko, O., Mileti, E., Raman, A., Bornholdt, J., Boyd, M., Toft, E., Qvist, V., Naslund, E., Thorell, A., Andersson, D. P., Dahlman, I., Gao, H., Sandelin, A., Daub, C. O., and Arner, P. (2016) The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity. Cell Rep, 16, 2317–2326.

Spoerry, C., Seele, J., Valentin-Weigand, P., Baums, C. G., and Pawel-Rammingen, U. von (2016) Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG . Journal of Biological Chemistry, 291, 7915–7925.

Stenson, M., Pedersen, A., Hasselblom, S., Nilsson-Ehle, H., Karlsson, B. G., Pinto, R., and Andersson, P.-O. (2016) Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients – a pilot study. Leukemia & Lymphoma, 57, 1814–1822.

Svennerholm, K., Rodsand, P., Hellman, U., Waldenstrom, A., Lundholm, M., Ahren, D., Biber, B., Ronquist, G., and Haney, M. (2016) DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning. PLoS ONE, 11, e0159105.

Teleman, J., Chawade, A., Sandin, M., Levander, F., and Malmström, J. (2016) Dinosaur: A Refined Open-Source Peptide MS Feature Detector. Journal of Proteome Research, 15, 2143–2151.

Thureborn, P., Franzetti, A., Lundin, D., and Sjöling, S. (2016) Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments. PeerJ, 4, e1593.

Tjernlund, A., Burgener, A., Lindvall, J. M., Peng, T., Zhu, J., Öhrmalm, L., Picker, L. J., Broliden, K., McElrath, M. J., and Corey, L. (2016) In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8\mathplus T cells—A Tool to Interrogate a Functional Immune Response Ex Vivo. PLOS ONE, 11, e0149907.

Uziela, K., Shu, N., Wallner, B., and Elofsson, A. (2016) ProQ3: Improved model quality assessments using Rosetta energy terms. Sci Rep, 6, 33509.

Wagner, R., Sydow, L. von, Aigner, H., Netotea, S., Brugière, S., Sjögren, L., Ferro, M., Clarke, A., and Funk, C. (2016) Deletion of FtsH11 protease has impact on chloroplast structure and function inArabidopsis thalianawhen grown under continuous light. Plant, Cell & Environment, 39, 2530–2544.

Wilkinson, M. D. et al. (2016) The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018.

Wrange, A.-L., Charrier, G., Thonig, A., Rosenblad, M. A., Blomberg, A., Havenhand, J. N., Jonsson, P. R., and André, C. (2016) The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854. PLOS ONE, 11, e0147082.

Zhou, Y., Frings, O., Branca, R. M., Boekel, J., Sage, C. le, Fredlund, E., Agami, R., and Orre, L. M. (2016) microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network. Oncogene.

2015

Alexeyenko, A., Alkasalias, T., Pavlova, T., Szekely, L., Kashuba, V., Rundqvist, H., Wiklund, P., Egevad, L., Csermely, P., Korcsmaros, T., Guven, H., and Klein, G. (2015) Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth. J. Exp. Clin. Cancer Res., 34, 62.

Bersani, C., Huss, M., Giacomello, S., Xu, L. D., Bianchi, J., Eriksson, S., Jerhammar, F., Alexeyenko, A., Vilborg, A., Lundeberg, J., Lui, W. O., and Wiman, K. G. (2015) Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis. Oncotarget, .

Boekel, J., Chilton, J. M., Cooke, I. R., Horvatovich, P. L., Jagtap, P. D., Kall, L., Lehtio, J., Lukasse, P., Moerland, P. D., and Griffin, T. J. (2015) Multi-omic data analysis using Galaxy. Nat. Biotechnol., 33, 137–139.

Chawade, A., Sandin, M., Teleman, J., Malmstrom, J., and Levander, F. (2015) Data processing has major impact on the outcome of quantitative label-free LC-MS analysis. J. Proteome Res., 14, 676–687.

Delhomme, N., Sundstrom, G., Zamani, N., Lantz, H., Lin, Y. C., Hvidsten, T. R., Hoppner, M. P., Jern, P., Peer, Y. Van de, Lundeberg, J., Grabherr, M. G., and Street, N. R. (2015) Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PLoS ONE, 10, e0139080.

Dmitriev, A. A., Rosenberg, E. E., Krasnov, G. S., Gerashchenko, G. V., Gordiyuk, V. V., Pavlova, T. V., Kudryavtseva, A. V., Beniaminov, A. D., Belova, A. A., Bondarenko, Y. N., Danilets, R. O., Glukhov, A. I., Kondratov, A. G., Alexeyenko, A., Alekseev, B. Y., Klein, G., Senchenko, V. N., and Kashuba, V. I. (2015) Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis. Dis. Markers, 2015, 241301.

Dumesic, P. A., Rosenblad, M. A., Samuelsson, T., Nguyen, T., Moresco, J. J., Yates, J. R., and Madhani, H. D. (2015) Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res., 43, 9017–9027.

Edo, M., Bjorn, E., Persson, P. E., and Jansson, S. (2015) Assessment of chemical and material contamination in waste wood fuels - A case study ranging over nine years. Waste Manag, .

Fall, T., Lundholm, C., Ortqvist, A. K., Fall, K., Fang, F., Hedhammar, A., Kampe, O., Ingelsson, E., and Almqvist, C. (2015) Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma. JAMA Pediatr, 169, e153219.

Freyhult, E., Gustafsson, M. G., and Strömbergsson, H. (2015) A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets. Mol. Inf., 34, 44–52.

Garcia, S. L., Buck, M., McMahon, K. D., Grossart, H. P., Eiler, A., and Warnecke, F. (2015) Auxotrophy and intrapopulation complementary in the ’interactome’ of a cultivated freshwater model community. Mol. Ecol., 24, 4449–4459.

Green, H., Hasmats, J., Kupershmidt, I., Edsgard, D., Petris, L. de, Lewensohn, R., Blackhall, F., Vikingsson, S., Besse, B., Lindgren, A., Branden, E., Koyi, H., Peterson, C., and Lundeberg, J. (2015) Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities. Clinical Cancer Research, 22, 366–373.

Herrmann, B., Isaksson, J., Ryberg, M., Tangrot, J., Saleh, I., Versteeg, B., Gravningen, K., and Bruisten, S. (2015) Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries. J. Clin. Microbiol., 53, 2172–2179.

Hosseini, S., Resjo, S., Liu, Y., Durling, M., Heyman, F., Levander, F., Liu, Y., Elfstrand, M., Funck Jensen, D., Andreasson, E., and Karlsson, M. (2015) Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae. J Proteomics, 117C, 24–40.

Hurst, L. D., Ghanbarian, A. T., Forrest, A. R., and Huminiecki, L. (2015) The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biol., 13, e1002315.

Kushwaha, S. K., Chauhan, P., Hedlund, K., and Ahrén, D. (2015) NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction. Bioinformatics, 32, 1223–1225.

Kushwaha, S. K., Manoharan, L., Meerupati, T., Hedlund, K., and Ahren, D. (2015) MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. BMC Bioinformatics, 16, 65.

Lamichhaney, S., Fan, G., Widemo, F., Gunnarsson, U., Thalmann, D. S., Hoeppner, M. P., Kerje, S., Gustafson, U., Shi, C., Zhang, H., Chen, W., Liang, X., Huang, L., Wang, J., Liang, E., Wu, Q., Lee, S. M.-Y., Xu, X., Höglund, J., Liu, X., and Andersson, L. (2015) Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nature Genetics, 48, 84–88.

Landegren, N., Sharon, D., Shum, A. K., Khan, I. S., Fasano, K. J., Hallgren, A., Kampf, C., Freyhult, E., Ardesjo-Lundgren, B., Alimohammadi, M., Rathsman, S., Ludvigsson, J. F., Lundh, D., Motrich, R., Rivero, V., Fong, L., Giwercman, A., Gustafsson, J., Perheentupa, J., Husebye, E. S., Anderson, M. S., Snyder, M., and Kampe, O. (2015) Transglutaminase 4 as a prostate autoantigen in male subfertility. Sci Transl Med, 7, 292ra101.

Lee, W., Alexeyenko, A., Pernemalm, M., Guegan, J., Dessen, P., Lazar, V., Lehtio, J., and Pawitan, Y. (2015) Identifying and Assessing Interesting Subgroups in a Heterogeneous Population. Biomed Res Int, 2015, 462549.

Leong, S. L., Lantz, H., Pettersson, O. V., Frisvad, J. C., Thrane, U., Heipieper, H. J., Dijksterhuis, J., Grabherr, M., Pettersson, M., Tellgren-Roth, C., and Schnurer, J. (2015) Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date. Environ. Microbiol., 17, 496–513.

Liang, C. et al. (2015) The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nat Commun, 6, 6066.

Lindblad, O., Li, T., Su, X., Sun, J., Kabir, N. N., Levander, F., Zhao, H., Lu, G., Ronnstrand, L., and Kazi, J. U. (2015) BEX1 acts as a tumor suppressor in acute myeloid leukemia. Oncotarget, 6, 21395–21405.

Malmstrom, L., Bakochi, A., Svensson, G., Kilsgard, O., Lantz, H., Petersson, A. C., Hauri, S., Karlsson, C., and Malmstrom, J. (2015) Quantitative proteogenomics of human pathogens using DIA-MS. J Proteomics, 129, 98–107.

Manoharan, L., Kushwaha, S. K., Hedlund, K., and Ahren, D. (2015) Captured metagenomics: large-scale targeting of genes based on ’sequence capture’ reveals functional diversity in soils. DNA Res., 451–460.

Mattsson, A., Karrman, A., Pinto, R., and Brunstrom, B. (2015) Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid (PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors. PLoS ONE, 10, e0143780.

Menzel, M., Sletvold, N., Agren, J., and Hansson, B. (2015) Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression. Mol. Biol. Evol., 32, 2036–2047.

Ohrvik, H. and Wittung-Stafshede, P. (2015) Identification of New Potential Interaction Partners for Human Cytoplasmic Copper Chaperone Atox1: Roles in Gene Regulation? Int J Mol Sci, 16, 16728–16739.

Peters, C., Tsirigos, K. D., Shu, N., and Elofsson, A. (2015) Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics, .

Prasad, M. A., Ungerback, J., Ahsberg, J., Somasundaram, R., Strid, T., Larsson, M., Mansson, R., De Paepe, A., Lilljebjorn, H., Fioretos, T., Hagman, J., and Sigvardsson, M. (2015) Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency. Blood, 125, 4052–4059.

Qi, D., Lawless, C., Teleman, J., Levander, F., Holman, S. W., Hubbard, S., and Jones, A. R. (2015) Representation of selected-reaction monitoring data in the mzQuantML data standard. Proteomics, 15, 2592–2596.

Rodriguez, S. A., Grochova, D., McKenna, T., Borate, B., Trivedi, N. S., Erdos, M. R., and Eriksson, M. (2015) Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging. Aging Cell, .

Ronquist, F., Nieves-Aldrey, J. L., Buffington, M. L., Liu, Z., Liljeblad, J., and Nylander, J. A. (2015) Phylogeny, evolution and classification of gall wasps: the plot thickens. PLoS ONE, 10, e0123301.

Ross, A. B., Svelander, C., Undeland, I., Pinto, R., and Sandberg, A. S. (2015) Herring and Beef Meals Lead to Differences in Plasma 2-Aminoadipic Acid, \beta-Alanine, 4-Hydroxyproline, Cetoleic Acid, and Docosahexaenoic Acid Concentrations in Overweight Men. J. Nutr., 145, 2456–2463.

Sandin, M., Chawade, A., and Levander, F. (2015) Is label-free LC-MS/MS ready for biomarker discovery? Proteomics Clin Appl, 9, 289–294.

Sanli, K., Bengtsson-Palme, J., Nilsson, R. H., Kristiansson, E., Alm Rosenblad, M., Blanck, H., and Eriksson, K. M. (2015) Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. Front Microbiol, 6, 1192.

Shah, F., Nicolás, C., Bentzer, J., Ellström, M., Smits, M., Rineau, F., Canbäck, B., Floudas, D., Carleer, R., Lackner, G., Braesel, J., Hoffmeister, D., Henrissat, B., Ahrén, D., Johansson, T., Hibbett, D. S., Martin, F., Persson, P., and Tunlid, A. (2015) Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. New Phytologist, 209, 1705–1719.

Silvar, C., Martis, M. M., Nussbaumer, T., Haag, N., Rauser, R., Keilwagen, J., Korzun, V., Mayer, K. F. X., Ordon, F., and Perovic, D. (2015) Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes. The Plant Genome, 8, 0.

Siretskiy, A., Sundqvist, T., Voznesenskiy, M., and Spjuth, O. (2015) A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data. Gigascience, 4, 26.

Skoglund, C., Carlsen, A. L., Weiner, M., Kurz, T., Hellmark, T., Eriksson, P., Heegaard, N. H., and Segelmark, M. (2015) Circulating microRNA expression pattern separates patients with anti-neutrophil cytoplasmic antibody associated vasculitis from healthy controls. Clin. Exp. Rheumatol., 33, 64–71.

Sommer, F., Nookaew, I., Sommer, N., Fogelstrand, P., and Backhed, F. (2015) Site-specific programming of the host epithelial transcriptome by the gut microbiota. Genome Biol., 16, 62.

Sooman, L., Freyhult, E., Jaiswal, A., Navani, S., Edqvist, P. H., Ponten, F., Tchougounova, E., Smits, A., Elsir, T., Gullbo, J., Lennartsson, J., Bergqvist, M., and Ekman, S. (2015) FGF2 as a potential prognostic biomarker for proneural glioma patients. Acta Oncol, 54, 385–394.

Spannagl, M., Nussbaumer, T., Bader, K. C., Martis, M. M., Seidel, M., Kugler, K. G., Gundlach, H., and Mayer, K. F. X. (2015) PGSB PlantsDB: updates to the database framework for comparative plant genome research. Nucleic Acids Research, 44, D1141–D1147.

Spjuth, O., Bongcam-Rudloff, E., Hernández, G. C., Forer, L., Giovacchini, M., Guimera, R. V., Kallio, A., Korpelainen, E., Kańduła, M. M., Krachunov, M., Kreil, D. P., Kulev, O., Łabaj, P. P., Lampa, S., Pireddu, L., Schönherr, S., Siretskiy, A., and Vassilev, D. (2015) Experiences with workflows for automating data-intensive bioinformatics. Biology Direct, 10.

Stella, R., Biancotto, G., Arrigoni, G., Barrucci, F., Angeletti, R., and James, P. (2015) Proteomics for the detection of indirect markers of steroids treatment in bovine muscle. PROTEOMICS.

Sundstrom, G., Zamani, N., Grabherr, M. G., and Mauceli, E. (2015) Whiteboard: a framework for the programmatic visualization of complex biological analyses. Bioinformatics, 31, 2054–2055.

Thuring, C., Follin, E., Geironson, L., Freyhult, E., Junghans, V., Harndahl, M., Buus, S., and Paulsson, K. M. (2015) HLA class I is most tightly linked to levels of tapasin compared with other antigen-processing proteins in glioblastoma. Br. J. Cancer, 113, 1640.

Tsirigos, K. D., Peters, C., Shu, N., Kall, L., and Elofsson, A. (2015) The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res., 43, W401–407.

Vigil-Stenman, T., Larsson, J., Nylander, J. A., and Bergman, B. (2015) Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis. BMC Genomics, 16, 193.

Wallace-Salinas, V., Brink, D. P., Ahren, D., and Gorwa-Grauslund, M. F. (2015) Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress. BMC Genomics, 16, 514.

Yoshihara, M. et al. (2015) Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PLoS ONE, 10, e0117581.

Zubair, S., Fischer, A., Liljander, A., Meens, J., Hegerman, J., Gourle, H., Bishop, R. P., Roebbelen, I., Younan, M., Mustafa, M. I., Mushtaq, M., Bongcam-Rudloff, E., and Jores, J. (2015) Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel. Stand Genomic Sci, 10, 109.

2014

Alkasalias, T., Flaberg, E., Kashuba, V., Alexeyenko, A., Pavlova, T., Savchenko, A., Szekely, L., Klein, G., and Guven, H. (2014) Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent. Proc. Natl. Acad. Sci. U.S.A., 111, 17188–17193.

Alneberg, J., Bjarnason, B. S., Bruijn, I. de, Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., and Quince, C. (2014) Binning metagenomic contigs by coverage and composition. Nat. Methods, .

Badea, S. L., Mustafa, M., Lundstedt, S., and Tysklind, M. (2014) Leachability and desorption of PCBs from soil and their dependency on pH and dissolved organic matter. Sci. Total Environ., 499C, 220–227.

Bengtsson-Palme, J., Alm Rosenblad, M., Molin, M., and Blomberg, A. (2014) Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. BMC Genomics, 15, 749.

Branca, R. M., Orre, L. M., Johansson, H. J., Granholm, V., Huss, M., Perez-Bercoff, A., Forshed, J., Kall, L., and Lehtio, J. (2014) HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat. Methods, 11, 59–62.

Browall, S., Norman, M., Tångrot, J., Galanis, I., Sjöström, K., Dagerhamn, J., Hellberg, C., Pathak, A., Spadafina, T., Sandgren, A., Bättig, P., Franzén, O., Andersson, B., Örtqvist, Å., Normark, S., and Henriques-Normark, B. (2014) Intraclonal Variations Among Streptococcus pneumoniae Isolates Influence the Likelihood of Invasive Disease in Children. Journal of Infectious Diseases, 209, 377–388.

Chawade, A., Alexandersson, E., and Levander, F. (2014) Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets. J. Proteome Res., 13, 3114–3120.

Chawade, A., Sandin, M., Teleman, J., Malmstrom, J., and Levander, F. (2014) Data processing has major impact on the outcome of quantitative label-free LC-MS analysis. J. Proteome Res., .

Delroisse, J., Ullrich-Luter, E., Ortega-Martinez, O., Dupont, S., Arnone, M. I., Mallefet, J., and Flammang, P. (2014) High opsin diversity in a non-visual infaunal brittle star. BMC Genomics, 15, 1035.

Dupont, C. L. et al. (2014) Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLoS ONE, 9, e89549.

Einarsdottir, B. O., Bagge, R. O., Bhadury, J., Jespersen, H., Mattsson, J., Nilsson, L. M., Truve, K., Lopez, M. D., Naredi, P., Nilsson, O., Stierner, U., Ny, L., and Nilsson, J. A. (2014) Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions. Oncotarget, 5, 9609–9618.

Ericson, P. G., Klopfstein, S., Irestedt, M., Nguyen, J. M., and Nylander, J. A. (2014) Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evol. Biol., 14, 8.

Hammerling, U., Freyhult, E., Edberg, A., Sand, S., Fagt, S., Knudsen, V. K., Andersen, L. F., Lindroos, A. K., Soeria-Atmadja, D., and Gustafsson, M. G. (2014) Identifying Food Consumption Patterns among Young Consumers by Unsupervised and Supervised Multivariate Data Analysis. European Journal of Nutrition & Food Safety, 4, 392–403.

Larsson, N., Lundstrom, S. L., Pinto, R., Rankin, G., Karimpour, M., Blomberg, A., Sandstrom, T., Pourazar, J., Trygg, J., Behndig, A. F., Wheelock, C. E., and Nording, M. L. (2014) Lipid mediator profiles differ between lung compartments in asthmatic and healthy humans. Eur. Respir. J., 43, 453–463.

Light, S., Basile, W., and Elofsson, A. (2014) Orphans and new gene origination, a structural and evolutionary perspective. Curr. Opin. Struct. Biol., 26, 73–83.

Magnusson, K., Simon, R., Sjölander, D., Sigurdson, C. J., Hammarström, P., and Nilsson, K. P. (2014) Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands. Prion, 8, .

Mahler, N., Cheregi, O., Funk, C., Netotea, S., and Hvidsten, T. R. (2014) Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803. PLoS ONE, 9, e113496.

Merid, S. K., Goranskaya, D., and Alexeyenko, A. (2014) Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis. BMC Bioinformatics, 15, 308.

Netotea, S., Sundell, D., Street, N. R., and Hvidsten, T. R. (2014) ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. BMC Genomics, 15, 106.

Nylinder, S., Lemey, P., De Bruyn, M., Suchard, M. A., Pfeil, B. E., Walsh, N., and Anderberg, A. A. (2014) On the biogeography of centipeda: a species-tree diffusion approach. Syst. Biol., 63, 178–191.

Panova, M., Johansson, T., Canback, B., Bentzer, J., Rosenblad, M. A., Johannesson, K., Tunlid, A., and Andre, C. (2014) Species and gene divergence in Littorina snails detected by array comparative genomic hybridization. BMC Genomics, 15, 687.

Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Muller, I., Baglione, V., Unneberg, P., Wikelski, M., Grabherr, M. G., and Wolf, J. B. (2014) The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344, 1410–1414.

Resjo, S., Ali, A., Meijer, H. J., Seidl, M. F., Snel, B., Sandin, M., Levander, F., Govers, F., and Andreasson, E. (2014) Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family. J. Proteome Res., 13, 1848–1859.

Saleiban, A., Faxalv, L., Claesson, K., Jonsson, J. I., and Osman, A. (2014) miR-20b regulates expression of PAR-1 thrombin receptor in melanoma cells. Pigment Cell Melanoma Res, 27, 431–441.

Sandin, M., Teleman, J., Malmström, J., and Levander, F. (2014) Data processing methods and quality control strategies for label-free LC–MS protein quantification . Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics , 1844, 29–41.

Sooman, L., Freyhult, E., Jaiswal, A., Navani, S., Edqvist, P. H., Ponten, F., Tchougounova, E., Smits, A., Elsir, T., Gullbo, J., Lennartsson, J., Bergqvist, M., and Ekman, S. (2014) FGF2 as a potential prognostic biomarker for proneural glioma patients. Acta Oncol, 1–10.

Teleman, J., Dowsey, A. W., Gonzalez-Galarza, F. F., Perkins, S., Pratt, B., Rost, H. L., Malmstrom, L., Malmstrom, J., Jones, A. R., Deutsch, E. W., and Levander, F. (2014) Numerical compression schemes for proteomics mass spectrometry data. Mol. Cell Proteomics, 13, 1537–1542.

Virkki, M., Boekel, C., Illergard, K., Peters, C., Shu, N., Tsirigos, K. D., Elofsson, A., Heijne, G. von, and Nilsson, I. (2014) Large tilts in transmembrane helices can be induced during tertiary structure formation. J. Mol. Biol., 426, 2529–2538.

Westram, A. M., Galindo, J., Alm Rosenblad, M., Grahame, J. W., Panova, M., and Butlin, R. K. (2014) Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations? Mol. Ecol., 23, 4603–4616.

Zovko, A., Novak, M., Hååg, P., Kovalerchick, D., Holmlund, T., Färnegårdh, K., Ilan, M., Carmeli, S., Lewensohn, R., and Viktorsson, K. (2014) Compounds from the marine sponge \lessi\greaterCribrochalina vasculum\less/i\greater offer a way to target IGF-1R mediated signaling in tumor cells. Oncotarget.

2013

Ahsberg, J., Ungerback, J., Strid, T., Welinder, E., Stjernberg, J., Larsson, M., Qian, H., and Sigvardsson, M. (2013) Early B-cell Factor 1 regulates the expansion of B-cell progenitors in a dose dependent manner. J. Biol. Chem., 288, 33449–33461.

Andersson, K. M., Meerupati, T., Levander, F., Friman, E., Ahren, D., and Tunlid, A. (2013) Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum. Appl. Environ. Microbiol., 79, 4993–5004.

Anna Edberg, Eva Freyhult, Salomon Sand, Sisse Fagt, Vibeke Kildegaard Knudsen, Lene Frost Andersen, Anna Karin Lindroos, Daniel Soeria-Atmadja, Mats G. Gustafsson and Hammerling, U. (2013) Discovery and characterisation of dietary patterns in two Nordic countries: Using non-supervised and supervised multivariate statistical techniques to analyse dietary survey data. TemaNord, 548.

Bendz, M., Skwark, M., Nilsson, D., Granholm, V., Cristobal, S., Käll, L., and Elofsson, A. (2013) Membrane protein shaving with thermolysin can be used to evaluate topology predictors. PROTEOMICS, 13, 1467–1480.

Butler, E., Alsterfjord, M., Olofsson, T., Karlsson, C., Malmstrom, J., and Vasquez, A. (2013) Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress. BMC Microbiology, 13, 235.

Hansen, K., Perry, B. A., Dranginis, A. W., and Pfister, D. H. (2013) A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits. Mol. Phylogenet. Evol., 67, 311–335.

Jornvall, H., Hedlund, J., Bergman, T., Kallberg, Y., Cederlund, E., and Persson, B. (2013) Origin and evolution of medium chain alcohol dehydrogenases. Chem. Biol. Interact., 202, 91–96.

Kontham, V., Holst, S. von, and Lindblom, A. (2013) Linkage analysis in familial non-lynch syndrome colorectal cancer families from sweden. PLoS ONE, 8, e83936.

Lampa, S., Dahlo, M., Olason, P. I., Hagberg, J., and Spjuth, O. (2013) Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. Gigascience, 2, 9.

Light, S. and Elofsson, A. (2013) The impact of splicing on protein domain architecture. Curr. Opin. Struct. Biol., 23, 451–458.

Light, S., Sagit, R., Ekman, D., and Elofsson, A. (2013) Long indels are disordered: A study of disorder and indels in homologous eukaryotic proteins. Biochim. Biophys. Acta, 1834, 890–897.

Light, S., Sagit, R., Sachenkova, O., Ekman, D., and Elofsson, A. (2013) Protein expansion is primarily due to indels in intrinsically disordered regions. Mol. Biol. Evol., 30, 2645–2653.

Lind, U., Alm Rosenblad, M., Wrange, A. L., Sundell, K. S., Jonsson, P. R., Andre, C., Havenhand, J., and Blomberg, A. (2013) Molecular characterization of the \alpha-subunit of Na^+/K^+ ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants. PLoS ONE, 8, e77069.

Mangold, S., Rao Jonna, V., and Dopson, M. (2013) Response of Acidithiobacillus caldus toward suboptimal pH conditions. Extremophiles, 17, 689–696.

Mayer, G., Montecchi-Palazzi, L., Ovelleiro, D., Jones, A. R., Binz, P.-A., Deutsch, E. W., Chambers, M., Kallhardt, M., Levander, F., Shofstahl, J., Orchard, S., Antonio Vizcaíno, J., Hermjakob, H., Stephan, C., Meyer, H. E., and Eisenacher, M. (2013) The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database, 2013.

Meerupati, T., Andersson, K. M., Friman, E., Kumar, D., Tunlid, A., and Ahren, D. (2013) Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi. PLoS Genet., 9, e1003909.

Nookaew, I., Svensson, P. A., Jacobson, P., Jernas, M., Taube, M., Larsson, I., Andersson-Assarsson, J. C., Sjostrom, L., Froguel, P., Walley, A., Nielsen, J., and Carlsson, L. M. (2013) Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men. J. Clin. Endocrinol. Metab., 98, E370–378.

Nookaew, I., Thorell, K., Worah, K., Wang, S., Lloyd Hibberd, M., Sjovall, H., Pettersson, S., Nielsen, J., and Lundin, S. B. (2013) Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker. BMC Med Genomics, 6, 41.

Nørholm, M. H., Toddo, S., Virkki, M. T., Light, S., Heijne, G. von, and Daley, D. O. (2013) Improved production of membrane proteins in Escherichia coli by selective codon substitutions. FEBS Lett., 587, 2352–2358.

Olsson, N., Carlsson, P., James, P., Hansson, K., Waldemarson, S., Malmstrom, P., Ferno, M., Ryden, L., Wingren, C., and Borrebaeck, C. A. (2013) Grading breast cancer tissues using molecular portraits. Mol. Cell Proteomics, 12, 3612–3623.

Persson, B. and Kallberg, Y. (2013) Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs). Chem. Biol. Interact., 202, 111–115.

Rosenblad, M. A., Trager, C., and Schunemann, D. (2013) Structural diversity of signal recognition particle RNAs in plastids. Plant Signal Behav, 8, doi: 10.4161/psb.26848.

Rowe, M., Laskemoen, T., Johnsen, A., and Lifjeld, J. T. (2013) Evolution of sperm structure and energetics in passerine birds. Proc. Biol. Sci., 280, 20122616.

Sandin, M., Ali, A., Hansson, K., Mansson, O., Andreasson, E., Resjo, S., and Levander, F. (2013) An Adaptive Alignment Algorithm for Quality-controlled Label-free LC-MS. Mol. Cell Proteomics, 12, 1407–1420.

Sanli, K., Karlsson, F. H., Nookaew, I., and Nielsen, J. (2013) FANTOM: Functional and taxonomic analysis of metagenomes. BMC Bioinformatics, 14, 38.

Sooman, L., Lennartsson, J., Gullbo, J., Bergqvist, M., Tsakonas, G., Johansson, F., Edqvist, P.-H., Pontén, F., Jaiswal, A., Navani, S., Alafuzoff, I., Popova, S., Blomquist, E., and Ekman, S. (2013) Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival. Medical oncology (Northwood, London, England), 30, 638.

Teleman, J., Waldemarson, S., Malmström, J., and Levander, F. (2013) Automated quality control system for LC-SRM setups . Journal of Proteomics , 95, 77–83.

Teschendorff, A. E., Marabita, F., Lechner, M., Bartlett, T., Tegner, J., Gomez-Cabrero, D., and Beck, S. (2013) A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics, 29, 189–196.

2012

Arabi, A., Ullah, K., Branca, R. M., Johansson, J., Bandarra, D., Haneklaus, M., Fu, J., Aries, I., Nilsson, P., Den Boer, M. L., Pokrovskaja, K., Grander, D., Xiao, G., Rocha, S., Lehtio, J., and Sangfelt, O. (2012) Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway. Nat Commun, 3, 976.

Carlsson, F., Trilling, M., Perez, F., and Ohlin, M. (2012) A dimerized single-chain variable fragment system for the assessment of neutralizing activity of phage display-selected antibody fragments specific for cytomegalovirus. J. Immunol. Methods, 376, 69–78.

Huminiecki, L. and Conant, G. C. (2012) Polyploidy and the evolution of complex traits. Int J Evol Biol, 2012, 292068.

Kallberg, Y., Segerstolpe, A., Lackmann, F., Persson, B., and Wieslander, L. (2012) Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function. PLoS ONE, 7, e43786.

Kirik, U., Cifani, P., Albrekt, A. S., Lindstedt, M., Heyden, A., and Levander, F. (2012) Multimodel pathway enrichment methods for functional evaluation of expression regulation. J. Proteome Res., 11, 2955–2967.

Larsson, S., Resjo, S., Gomez, M. F., James, P., and Holm, C. (2012) Characterization of the lipid droplet proteome of a clonal insulin-producing β-cell line (INS-1 832/13). J. Proteome Res., 11, 1264–1273.

Light, S., Sagit, R., Ithychanda, S. S., Qin, J., and Elofsson, A. (2012) The evolution of filamin - a protein domain repeat perspective. J. Struct. Biol., 179, 289–298.

Lundin, D., Severin, I., Logue, J. B., Ostman, O., Andersson, A. F., and Lindstrom, E. S. (2012) Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity? Environ Microbiol Rep, 4, 367–372.

Moummou, H., Kallberg, Y., Tonfack, L. B., Persson, B., and Rest, B. van der (2012) The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns. BMC Plant Biol., 12, 219.

Nilsson, R. H., Tedersoo, L., Abarenkov, K., Ryberg, M., Kristiansson, E., Hartmann, M., Schoch, C. L., Nylander, J. A. A., Bergsten, J., Porter, T. M., Jumpponen, A., Vaishampayan, P., Ovaskainen, O., Hallenberg, N., Bengtsson-Palme, J., Eriksson, K. M., Larsson, K.-H., Larsson, E., and Koeljalg, U. (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys, 4, 37–63.

Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlen, M., and Nielsen, J. (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res., 40, 10084–10097.

Nørholm, M. H., Light, S., Virkki, M. T., Elofsson, A., Heijne, G. von, and Daley, D. O. (2012) Manipulating the genetic code for membrane protein production: What have we learnt so far? Biochim. Biophys. Acta, 1818, 1091–1096.

Olsson, N., James, P., Borrebaeck, C. A., and Wingren, C. (2012) Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry. Mol. Cell Proteomics, 11, 342–354.

Olsson, N., Wallin, S., James, P., Borrebaeck, C. A. K., and Wingren, C. (2012) Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties. Protein Science, 21, 1897–1910.

Papini, M., Nookaew, I., Uhlen, M., and Nielsen, J. (2012) Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae. Microb. Cell Fact., 11, 136.

Pinto, R. C., Gerber, L., Eliasson, M., Sundberg, B., and Trygg, J. (2012) Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis. Anal. Chem., 84, 8675–8681.

Teleman, J., Karlsson, C., Waldemarson, S., Hansson, K., James, P., Malmström, J., and Levander, F. (2012) Automated selected reaction monitoring software for accurate label-free protein quantification. J. Proteome Res., 11, 3766–3773.

Trager, C., Rosenblad, M. A., Ziehe, D., Garcia-Petit, C., Schrader, L., Kock, K., Richter, C. V., Klinkert, B., Narberhaus, F., Herrmann, C., Hofmann, E., Aronsson, H., and Schunemann, D. (2012) Evolution from the prokaryotic to the higher plant chloroplast signal recognition particle: the signal recognition particle RNA is conserved in plastids of a wide range of photosynthetic organisms. Plant Cell, 24, 4819–4836.

2011

Olsson, N., Wingren, C., Mattsson, M., James, P., O’Connell, D., Nilsson, F., Cahill, D. J., and Borrebaeck, C. A. (2011) Proteomic analysis and discovery using affinity proteomics and mass spectrometry. Mol. Cell Proteomics, 10, M110.003962.