BILS publications


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.


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.

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