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  • 1.
    Alneberg, Johannes
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bjarnason, Brynjar Smári
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    de Bruijn, Ino
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Bioinformatics Infrastructure for Life Sciences (BILS), Sweden.
    Schirmer, Melanie
    Quick, Joshua
    Ijaz, Umer Z.
    Lahti, Leo
    Loman, Nicholas J.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Quince, Christopher
    Binning metagenomic contigs by coverage and composition2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 11, p. 1144-1146Article in journal (Refereed)
    Abstract [en]

    Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

  • 2. Bieniossek, Christoph
    et al.
    Nie, Yan
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Frey, Daniel
    Olieric, Natacha
    Schaffitzel, Christiane
    Collinson, Ian
    Romier, Christophe
    Berger, Philipp
    Richmond, Timothy J.
    Steinmetz, Michel O.
    Berger, Imre
    Automated unrestricted multigene recombineering for multiprotein complex production2009In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 6, no 6, p. 447-U68Article in journal (Refereed)
    Abstract [en]

    Structural and functional studies of many multiprotein complexes depend on recombinant-protein overexpression. Rapid revision of expression experiments and diversification of the complexes are often crucial for success of these projects; therefore, automation is increasingly indispensable. We introduce Acembl, a versatile and automatable system for protein-complex expression in Escherichia coli that uses recombineering to facilitate multigene assembly and diversification. We demonstrated protein-complex expression using Acembl, including production of the complete prokaryotic holotranslocon.

  • 3. Branca, Rui M. M.
    et al.
    Orre, Lukas M.
    Johansson, Henrik J.
    Granholm, Viktor
    Huss, Mikael
    Perez-Bercoff, Åsa
    Forshed, Jenny
    Käll, Lukas
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lehtiö, Janne
    HiRIEF LC-MSMS enables deep proteome coverage and unbiased proteogenomics2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 1, p. 59-Article in journal (Refereed)
    Abstract [en]

    We present a liquid chromatography-mass spectrometry (LC-MSMS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.

  • 4. Chenouard, Nicolas
    et al.
    Smal, Ihor
    de Chaumont, Fabrice
    Maska, Martin
    Sbalzarini, Ivo F.
    Gong, Yuanhao
    Cardinale, Janick
    Carthel, Craig
    Coraluppi, Stefano
    Winter, Mark
    Cohen, Andrew R.
    Godinez, William J.
    Rohr, Karl
    Kalaidzidis, Yannis
    Liang, Liang
    Duncan, James
    Shen, Hongying
    Xu, Yingke
    Magnusson, Klas E. G.
    KTH, School of Electrical Engineering (EES), Signal Processing. KTH, School of Electrical Engineering (EES), Centres, ACCESS Linnaeus Centre.
    Jaldén, Joakim
    KTH, School of Electrical Engineering (EES), Signal Processing. KTH, School of Electrical Engineering (EES), Centres, ACCESS Linnaeus Centre.
    Blau, Helen M.
    Paul-Gilloteaux, Perrine
    Roudot, Philippe
    Kervrann, Charles
    Waharte, Francois
    Tinevez, Jean-Yves
    Shorte, Spencer L.
    Willemse, Joost
    Celler, Katherine
    van Wezel, Gilles P.
    Dan, Han-Wei
    Tsai, Yuh-Show
    Ortiz de Solorzano, Carlos
    Olivo-Marin, Jean-Christophe
    Meijering, Erik
    Objective comparison of particle tracking methods2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 3, p. 281-U247Article in journal (Refereed)
    Abstract [en]

    Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Because manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized an open competition in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers.

  • 5. Colwill, Karen
    et al.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Sundberg, Mårten
    KTH, School of Biotechnology (BIO), Proteomics.
    Sjöberg, Ronald
    KTH, School of Biotechnology (BIO), Proteomics.
    Sivertsson, Åsa
    KTH, School of Biotechnology (BIO), Proteomics.
    Schwenk, Jochen M
    KTH, School of Biotechnology (BIO), Proteomics.
    Ottosson Takanen, Jenny
    KTH, School of Biotechnology (BIO), Proteomics.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Gräslund, Susanne
    et, al.
    A roadmap to generate renewable protein binders to the human proteome2011In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 8, no 7, p. 551-8Article in journal (Refereed)
    Abstract [en]

    Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.

  • 6. Frauenfeld, Jens
    et al.
    Loving, Robin
    Armache, Jean-Paul
    Sonnen, Andreas F-P
    Guettou, Fatma
    Moberg, Per
    Zhu, Lin
    KTH, School of Technology and Health (STH), Health Systems Engineering.
    Jegerschöld, Caroline
    KTH, School of Technology and Health (STH), Basic Science and Biomedicine, Structural Biotechnology.
    Flayhan, Ali
    Briggs, John A. G.
    Garoff, Henrik
    Low, Christian
    Cheng, Yifan
    Nordlund, Par
    A saposin-lipoprotein nanoparticle system for membrane proteins2016In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 13, no 4, p. 345-351Article in journal (Refereed)
    Abstract [en]

    A limiting factor in membrane protein research is the ability to solubilize and stabilize such proteins. Detergents are used most often for solubilizing membrane proteins, but they are associated with protein instability and poor compatibility with structural and biophysical studies. Here we present a saposin-lipoprotein nanoparticle system, Salipro, which allows for the reconstitution of membrane proteins in a lipid environment that is stabilized by a scaffold of saposin proteins. We demonstrate the applicability of the method on two purified membrane protein complexes as well as by the direct solubilization and nanoparticle incorporation of a viral membrane protein complex from the virus membrane. Our approach facilitated high-resolution structural studies of the bacterial peptide transporter PeptT(S02) by single-particle cryo-electron microscopy (cryo-EM) and allowed us to stabilize the HIV envelope glycoprotein in a functional state.

  • 7. Henriksson, Johan
    et al.
    Hench, Jurgen
    Tong, Yong Guang
    Johansson, Arvid
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Johansson, David
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Burglin, Thomas R.
    Endrov: an integrated platform for image analysis2013In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, no 6, p. 454-456Article in journal (Refereed)
  • 8.
    Käll, Lukas
    et al.
    Department of Genome Sciences, University of Washington.
    Canterbury, Jesse D.
    Weston, Jason
    Noble, William Stafford
    MacCoss, Michael J.
    Semi-supervised learning for peptide identification from shotgun proteomics datasets2007In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 4, no 11, p. 923-925Article in journal (Refereed)
    Abstract [en]

    Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of confident peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic Saccharomyces cerevisiae dataset, and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach.

  • 9.
    Pennacchietti, Francesca
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Serebrovskaya, Ekaterina O.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Faro, Aline R.
    Albert Einstein Coll Med, Dept Anat & Struct Biol, Bronx, NY 10467 USA.;Albert Einstein Coll Med, Gruss Lipper Biophoton Ctr, Bronx, NY 10467 USA..
    Shemyakina, Irina I.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Bozhanova, Nina G.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Kotlobay, Alexey A.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Gurskaya, Nadya G.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Bodén, Andreas
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Dreier, Jes
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Chudakov, Dmitry M.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Lukyanov, Konstantin A.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Verkhusha, Vladislav V.
    Albert Einstein Coll Med, Dept Anat & Struct Biol, Bronx, NY 10467 USA.;Albert Einstein Coll Med, Gruss Lipper Biophoton Ctr, Bronx, NY 10467 USA..
    Mishin, Alexander S.
    Russian Acad Sci, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow, Russia..
    Testa, Ilaria
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy2018In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 15, no 8, p. 601-+Article in journal (Refereed)
    Abstract [en]

    Reversibly photoswitchable fluorescent proteins (rsFPs) are gaining popularity as tags for optical nanoscopy because they make it possible to image with lower light doses. However, green rsFPs need violet-blue light for photoswitching, which is potentially phototoxic and highly scattering. We developed new rsFPs based on FusionRed that are reversibly photoswitchable with green-orange light. The rsFusionReds are bright and exhibit rapid photoswitching, thereby enabling nanoscale imaging of living cells.

  • 10.
    Rockberg, Johan
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Löfblom, John
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Hjelm, Barbara
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Epitope mapping of antibodies using bacterial surface display2008In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 5, no 12, p. 1039-1045Article in journal (Refereed)
    Abstract [en]

    We describe a method for mapping the epitopes recognized by antibodies, based on bacterial surface expression of antigen protein fragments followed by antibody-based flow-cytometric sorting. We analyzed the binding sites of both monoclonal and polyclonal antibodies directed to three human protein targets: (i) the human epidermal growth factor receptor 2 (HER2), (ii) ephrin-B3 and (iii) the transcription factor SATB2. All monoclonal antibodies bound a single epitope, whereas the polyclonal antibodies showed, in each case, a binding pattern with one to five separate epitopes. A comparison of polyclonal and monoclonal antibodies raised to the same antigen showed overlapping binding epitopes. We also demonstrated that bacterial cells with displayed protein fragments can be used as affinity ligands to generate epitope-specific antibodies. Our approach shows a path forward for systematic validation of antibodies for epitope specificity and cross-reactivity on a whole-proteome level.

  • 11.
    Stadler, Charlotte
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rexhepaj, Elton
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Singan, Vasanth R.
    Murphy, Robert F.
    Pepperkok, Rainer
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Simpson, Jeremy C.
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells2013In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, no 4, p. 315-323Article in journal (Refereed)
    Abstract [en]

    Imaging techniques such as immunofluorescence (IF) and the expression of fluorescent protein (FP) fusions are widely used to investigate the subcellular distribution of proteins. Here we report a systematic analysis of >500 human proteins comparing the localizations obtained in live versus fixed cells using FPs and IF, respectively. We identify systematic discrepancies between IF and FPs as well as between FP tagging at the N and C termini. The analysis shows that for 80% of the proteins, IF and FPs yield the same subcellular distribution, and the locations of 250 previously unlocalized proteins were determined by the overlap between the two methods. Approximately 60% of proteins localize to multiple organelles for both methods, indicating a complex subcellular protein organization. These results show that both IF and FP tagging are reliable techniques and demonstrate the usefulness of an integrative approach for a complete investigation of the subcellular human proteome.

  • 12. Stoeckius, Marlon
    et al.
    Maaskola, Jonas
    Max Delbrück Center for Molecular Medicine, Germany.
    Colombo, Teresa
    Rahn, Hans-Peter
    Friedländer, Marc R
    Li, Na
    Chen, Wei
    Piano, Fabio
    Rajewsky, Nikolaus
    Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.2009In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 6, no 10Article in journal (Refereed)
    Abstract [en]

    Caenorhabditis elegans is one of the most prominent model systems for embryogenesis, but collecting many precisely staged embryos has been impractical. Thus, early C. elegans embryogenesis has not been amenable to most high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect staged C. elegans embryos by fluorescence-activated cell sorting (eFACS). In a proof-of-principle experiment, we found that a single eFACS run routinely yielded tens of thousands of almost perfectly staged 1-cell stage embryos. As the earliest embryonic events are driven by posttranscriptional regulation, we combined eFACS with second-generation sequencing to profile the embryonic expression of small, noncoding RNAs. We discovered complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including microRNAs and 26G-RNAs, during embryogenesis.

  • 13. Taussig, Michael J.
    et al.
    Stoevesandt, Oda
    Borrebaeck, Carl A. K.
    Bradbury, Andrew R.
    Cahill, Dolores
    Cambillau, Christian
    de Daruvar, Antoine
    Duebel, Stefan
    Eichler, Jutta
    Frank, Ronald
    Gibson, Toby J.
    Gloriam, David
    Gold, Larry
    Herberg, Friedrich W.
    Hermjakob, Henning
    D Hoheisel, Joerg
    O Joos, Thomas
    Kallioniemi, Olli
    Koegll, Manfred
    Konthur, Zoltan
    Korn, Bernhard
    Kremmer, Elisabeth
    Krobitsch, Sylvia
    Landegren, Ulf
    van der Maarel, Silvere
    McCafferty, John
    Muyldermans, Serge
    Nygren, Per-Åke
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Palcy, Sandrine
    Plueckthun, Andreas
    Polic, Bojan
    Przybylski, Michael
    Saviranta, Petri
    Sawyer, Alan
    Sherman, David J.
    Skerra, Arne
    Templin, Markus
    Ueffing, Marius
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome2007In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 4, no 1, p. 13-17Article in journal (Refereed)
    Abstract [en]

    ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination.

  • 14.
    Uhlen, Mathias
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bandrowski, Anita
    Carr, Steven
    Edwards, Aled
    Ellenberg, Jan
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Rimm, David L.
    Rodriguez, Henry
    Hiltke, Tara
    Snyder, Michael
    Yamamoto, Tadashi
    A proposal for validation of antibodies2016In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 13, no 10, p. 823-+Article in journal (Other academic)
    Abstract [en]

    We convened an ad hoc International Working Group for Antibody Validation in order to formulate the best approaches for validating antibodies used in common research applications and to provide guidelines that ensure antibody reproducibility. We recommend five conceptual 'pillars' for antibody validation to be used in an application-specific manner.

  • 15.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Should we ignore western blots when selecting antibodies for other applications?2017In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 14, no 3, p. 215-216Article in journal (Refereed)
  • 16.
    Uhlén, Mathias
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bandrowski, A.
    Carr, S.
    Edwards, A.
    Ellenberg, J.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rimm, D. L.
    Rodriguez, H.
    Hiltke, T.
    Snyder, M.
    Yamamoto, T.
    A proposal for validation of antibodies2016In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 13, no 10, p. 823-827Article in journal (Refereed)
  • 17.
    Uhlén, Mathias
    et al.
    KTH, School of Biotechnology (BIO), Proteomics.
    Gräslund, Susanne
    Sundstroem, Michael
    A pilot project to generate affinity reagents to human proteins2008In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 5, no 10, p. 854-855Article in journal (Refereed)
  • 18. Ulman, V
    et al.
    Magnusson, Klas E. G.
    KTH, School of Electrical Engineering (EES), Centres, ACCESS Linnaeus Centre.
    Jaldén, Joakim
    KTH, School of Electrical Engineering (EES), Information Science and Engineering. KTH, School of Electrical Engineering (EES), Centres, ACCESS Linnaeus Centre.
    Ortiz-de-Solorzano, Carlos
    et al.,
    An objective comparison of cell-tracking algorithms2017In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 14, no 12, p. 1141-+Article in journal (Refereed)
    Abstract [en]

    We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge.

1 - 18 of 18
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