Publications

[1]

Jahn, M., Vialas, V., Karlsen, J., Maddalo, G., Edfors, F., Forsström, B. ... Hudson, E. P. (2018). Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins. Cell reports, 25(2), 478-+.

[2]

The, M., Edfors, F., Perez-Riverol, Y., Payne, S. H., Hoopmann, M. R., Palmblad, M. ... Käll, L. (2018). A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms. Journal of Proteome Research, 17(5), 1879-1886.

[3]

Thul, P., Åkesson, L., Mahdessian, D., Bäckström, A., Danielsson, F., Gnann, C. ... Lundberg, E. (2017). Exploring the Proteome of Multilocalizing Proteins. Molecular Biology of the Cell, 28.

[4]

Sjöstedt, E., Sivertsson, Å., Norradin, F. H., Katona, B., Näsström, Å., Vuu, J. ... Lindskog, C. (2018). Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues. Journal of Proteome Research, 17(12), 4127-4137.

[5]

Shabestary, K., Anfelt, J., Ljungqvist, E., Jahn, M., Yao, L. & Hudson, E. P. (2018). Targeted Repression of Essential Genes To Arrest Growth and Increase Carbon Partitioning and Biofuel Titers in Cyanobacteria. ACS Synthetic Biology, 7(7).

[6]

Fasterius, E., Uhlén, M., Al-Khalili Szigyarto, C. (). Single cell RNA-seq variant analysis for exploration of inter- and intra-tumour genetic heterogeneity. (Manuscript).

[7]

Kennedy, S., Fasterius, E., Al-Khalili Szigyarto, C., Kolch, W., et al., (). Adaptive rewiring of protein-protein interactions and signal flow in the EGFR signaling network by mutant RAS. (Manuscript).

[8]

Spitali, P., Hettne, K., Tsonaka, R., Charrout, M., van den Bergen, J., Koeks, Z. ... Aartsma-Rus, A. (2018). Tracking disease progression non-invasively in Duchenne and Becker muscular dystrophies. Journal of Cachexia, Sarcopenia and Muscle, 9(4), 715-726.

[9]

Alm, T. L., von Feilitzen, K. & Uhlén, M. (2015). Antibodypedia - The wiki of antibodies. Molecular Biology of the Cell, 26.

[10]

Janasch, M., Asplund-Samuelsson, J., Steuer, R. & Hudson, E. P. (2019). Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation. Journal of Experimental Botany, 70(3), 973-983.

[11]

Sjöstedt, E., Fagerberg, L., Mitsios, N., Adori, C., Oksvold, P., Limiszewka, A., Kheder, S., Norradin, F. H., Lindskog, C., Pontén, F., Hökfelt, T., Uhlén, M., Mulder, J. (). The transcriptomic landscape of mammalian brain. (Manuscript).

[12]

Karnevi, E., Dror, L. B., Mardinoglu, A., Elebro, J., Heby, M., Olofsson, S. -. ... Jirström, K. (2018). Translational study reveals a two-faced role of RBM3 in pancreatic cancer and suggests its potential value as a biomarker for improved patient stratification. OncoTarget, 9(5), 6188-6200.

[13]

Zhang, C., Bidkhori, G., Benfeitas, R., Lee, S., Arif, M., Uhlen, M. & Mardinoglu, A. (2018). ESS : A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling. Frontiers in Physiology, 9.

[14]

Karlsen, J., Asplund-Samuelsson, J., Thomas, Q., Jahn, M. & Hudson, E. P. (2018). Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation. MSYSTEMS, 3(5).

[15]

Sjöstedt, E. (2018). Towards a deeper understanding of the human brain (Doctoral thesis , KTH Royal Institute of Technology, Stockholm, TRITA-CBH-FOU 50). Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-235670.

[16]

Fasterius, E. (). seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data. (Manuscript).

[17]

Steen, J., Forsström, B., Sahlström, P., Odowd, V., Israelsson, L., Krishnamurthy, A. ... Malmstrom, V. (2019). Recognition of Amino Acid Motifs, Rather Than Specific Proteins, by Human Plasma Cell-Derived Monoclonal Antibodies to Posttranslationally Modified Proteins in Rheumatoid Arthritis. Arthritis & Rheumatology, 71(2), 196-209.

[18]

Benfeitas, R., Bidkhori, G., Mukhopadhyay, B., Klevstig, M., Arif, M., Zhang, C. ... Mardinoglu, A. (2019). Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis. EBioMedicine.

[19]

Neiman, M., Hellström, C., Just, D., Mattsson, C., Fagerberg, L., Schuppe-Koistinen, I. ... Nilsson, P. (2019). Individual and stable autoantibody repertoires in healthy individuals. Autoimmunity, 52(1), 1-11.

[20]

Cengic, I. (2019). Synthetic biology approaches for improving production of fatty acid-derived compounds in cyanobacteria (Doctoral thesis , KTH Royal Institute of Technology, Stockholm, TRITA-CBH-FOU 2019:16). Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-249935.

[21]

Lee, S., Zhang, C., Arif, M., Liu, Z., Benfeitas, R., Bidkhori, G. ... Mardinoglu, A. (2017). TCSBN: a database of tissue and cancer specific biological networks. Nucleic Acids Research.

[22]

Cengic, I., Sundh, J., Ininbergs, K., Bergman, B., Hudson, E. P. (). Evaluation of Baltic Sea metagenome-derived aldehyde deformylating oxygenases in Synechocystis sp. strain PCC 6803. (Manuscript).

[23]

Cengic, I., Asplund-Samuelsson, J., Hudson, E. P. (). Indications of differential transcriptional regulation of fatty acid synthesis in the model cyanobacteria Synechocystis sp. Strain PCC 6803 and Synechococcus elongatus PCC 7942. (Manuscript).

[24]

Turanli, B., Zhang, C., Kim, W., Benfeitas, R., Uhlén, M., Yalcin Arga, K. & Mardinoglu, A. (2019). Discovery of therapeutic agents for prostate cancer using genome-scale metabolic modeling and drug repositioning. EBioMedicine, 42, 386-396.

[25]

Liu, Z., Zhang, C., Lee, S., Kim, W., Klevstig, M., Harzandi, A. M. ... Mardinoglu, A. (2019). Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function. Metabolic engineering.

[26]

Klemencic, M., Asplund-Samuelsson, J., Dolinar, M. & Funk, C. (2019). Phylogenetic distribution and diversity of bacterial pseudo-orthocaspases underline their putative role in photosynthesis. Frontiers in Plant Science, 10.

[27]

Fasterius, E. & Al-Khalili Szigyarto, C. (2018). Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations. Scientific Reports, 8.

[28]

Edfors, F., Forsström, B., Vunk, H., Kotol, D., Fredolini, C., Maddalo, G. ... Uhlén, M. (2019). Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics. Journal of Proteome Research, 18(7), 2706-2718.

[29]

Häussler, R. S., Bendes, A., Iglesias, M. J., Sanchez-Rivera, L., Dodig-Crnkovic, T., Byström, S. ... Schwenk, J. M. (2019). Systematic Development of Sandwich Immunoassays for the Plasma Secretome. Proteomics.

[30]

Fasterius, E., Uhlén, M. & Al-Khalili Szigyarto, C. (2019). Single-cell RNA-seq variant analysis for exploration of genetic heterogeneity in cancer. Scientific Reports, 9.

[31]

Charitou, T., Srihari, S., Lynn, M. A., Jarboui, M.-A., Fasterius, E., Moldovan, M. ... Lynn, D. J. (2019). Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS(G13D) mutation. British Journal of Cancer, 121(1), 37-50.