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  • 1. Adler, Jeremy
    et al.
    Shevchuk, Andrew I
    Novak, Pavel
    Korchev, Yuri E
    Parmryd, Ingela
    Plasma membrane topography and interpretation of single-particle tracks.2010In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 7, no 3, p. 170-1Article in journal (Refereed)
  • 2.
    Andersson, Malin
    et al.
    Vanderbilt University.
    Groseclose, M Reid
    Deutch, Ariel Y
    Caprioli, Richard M
    Imaging mass spectrometry of proteins and peptides: 3D volume reconstruction.2008In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 5, no 1, p. 101-8Article in journal (Refereed)
    Abstract [en]

    As large genomic and proteomic datasets are generated from homogenates of various tissues, the need for information on the spatial localization of their encoded products has become more pressing. Matrix-assisted laser desorption-ionization (MALDI) imaging mass spectrometry (IMS) offers investigators the means with which to unambiguously study peptides and proteins with molecular specificity, and to determine their distribution in two and three dimensions. In the past few years, several parameters have been optimized for IMS, including sample preparation, matrix application and instrumental acquisition parameters (Box 1). These developments have resulted in a high degree of reproducibility in mass accuracy and peak intensities (Supplementary Fig. 1 online). Recently, we have optimized our protocol to be able to increase the number of molecular species analyzed by collecting two sets of sections, covering one set of sections with sinapinic acid for optimal detection of proteins and adjacent sections with 2,5-dihydroxybenzoic acid (DHB) matrix for the optimal detection of low-mass species, including peptides. Approximately 1,000 peaks can be observed in each dataset (Fig. 1). Furthermore, the sections are collected at an equal distance, 200 mum instead of 400-500 mum used previously, thus enabling the use of virtual z-stacks and three-dimensional (3D) volume renderings to investigate differential localization patterns in much smaller brain structures such as the substantia nigra and the interpeduncular nucleus. Here we present our optimized step-by-step procedure based on previous work in our laboratory, describing how to make 3D volume reconstructions of MALDI IMS data, as applied to the rat brain.

  • 3. Arnlund, David
    et al.
    Johansson, Linda C
    Wickstrand, Cecilia
    Barty, Anton
    Williams, Garth J
    Malmerberg, Erik
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Milathianaki, Despina
    DePonte, Daniel P
    Shoeman, Robert L
    Wang, Dingjie
    James, Daniel
    Katona, Gergely
    Westenhoff, Sebastian
    White, Thomas A
    Aquila, Andrew
    Bari, Sadia
    Berntsen, Peter
    Bogan, Mike
    van Driel, Tim Brandt
    Doak, R Bruce
    Kjær, Kasper Skov
    Frank, Matthias
    Fromme, Raimund
    Grotjohann, Ingo
    Henning, Robert
    Hunter, Mark S
    Kirian, Richard A
    Kosheleva, Irina
    Kupitz, Christopher
    Liang, Mengning
    Martin, Andrew V
    Nielsen, Martin Meedom
    Messerschmidt, Marc
    Seibert, M Marvin
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA..
    Sjöhamn, Jennie
    Stellato, Francesco
    Weierstall, Uwe
    Zatsepin, Nadia A
    Spence, John C H
    Fromme, Petra
    Schlichting, Ilme
    Boutet, Sébastien
    Groenhof, Gerrit
    Chapman, Henry N
    Neutze, Richard
    Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 9, p. 923-926Article in journal (Refereed)
    Abstract [en]

    We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.

  • 4. Bustin, Stephen A.
    et al.
    Benes, Vladimir
    Garson, Jeremy
    Hellemans, Jan
    Huggett, Jim
    Kubista, Mikael
    Mueller, Reinhold
    Nolan, Tania
    Pfaffl, Michael W.
    Shipley, Gregory
    Wittwer, Carl T.
    Schjerling, Peter
    Day, Philip J.
    Abreu, Monica
    Aguado, Begona
    Beaulieu, Jean-Francois
    Beckers, Anneleen
    Bogaert, Sara
    Browne, John A.
    Carrasco-Ramiro, Fernando
    Ceelen, Liesbeth
    Ciborowski, Kate
    Cornillie, Pieter
    Coulon, Stephanie
    Cuypers, Ann
    De Brouwer, Sara
    De Ceuninck, Leentje
    De Craene, Jurgen
    De Naeyer, Helene
    De Spiegelaere, Ward
    Deckers, Kato
    Dheedene, Annelies
    Durinck, Kaat
    Ferreira-Teixeira, Margarida
    Fieuw, Annelies
    Gallup, Jack M.
    Gonzalo-Flores, Sandra
    Goossens, Karen
    Heindryckx, Femke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Herring, Elizabeth
    Hoenicka, Hans
    Icardi, Laura
    Jaggi, Rolf
    Javad, Farzad
    Karampelias, Michael
    Kibenge, Frederick
    Kibenge, Molly
    Kumps, Candy
    Lambertz, Irina
    Lammens, Tim
    Markey, Amelia
    Messiaen, Peter
    Mets, Evelien
    Morais, Sofia
    Mudarra-Rubio, Alberto
    Nakiwala, Justine
    Nelis, Hilde
    Olsvik, Pal A.
    Perez-Novo, Claudina
    Plusquin, Michelle
    Remans, Tony
    Rihani, Ali
    Rodrigues-Santos, Paulo
    Rondou, Pieter
    Sanders, Rebecca
    Schmidt-Bleek, Katharina
    Skovgaard, Kerstin
    Smeets, Karen
    Tabera, Laura
    Toegel, Stefan
    Van Acker, Tim
    Van den Broeck, Wim
    Van der Meulen, Joni
    Van Gele, Mireille
    Van Peer, Gert
    Van Poucke, Mario
    Van Roy, Nadine
    Vergult, Sarah
    Wauman, Joris
    Tshuikina-Wiklander, Marina
    Willems, Erik
    Zaccara, Sara
    Zeka, Fjoralba
    Vandesompele, Jo
    The need for transparency and good practices in the qPCR literature2013In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, no 11, p. 1063-1067Article in journal (Other academic)
    Abstract [en]

    Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.

  • 5. Chen, Doris
    et al.
    Ahlford, Annika
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
    Schnorrer, Frank
    Kalchhauser, Irene
    Fellner, Michaela
    Viràgh, Erika
    Kiss, Istvàn
    Syvänen, Ann-Christine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
    Dickson, Barry J
    High-resolution, high-throughput SNP mapping in Drosophila melanogaster2008In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 5, no 4, p. 323-329Article in journal (Refereed)
    Abstract [en]

    Single nucleotide polymorphisms (SNPs) are useful markers for genetic mapping experiments in model organisms. Here we report the establishment of a high-density SNP map and high-throughput genotyping assays for Drosophila melanogaster. Our map comprises 27,367 SNPs in common laboratory Drosophila stocks. These SNPs were clustered within 2,238 amplifiable markers at an average density of 1 marker every 50.3 kb, or 6.3 genes. We have also constructed a set of 62 Drosophila stocks, each of which facilitates the generation of recombinants within a defined genetic interval of 1-2 Mb. For flexible, high-throughput SNP genotyping, we used fluorescent tag-array mini-sequencing (TAMS) assays. We designed and validated TAMS assays for 293 SNPs at an average resolution of 391.3 kb, and demonstrated the utility of these tools by rapidly mapping 14 mutations that disrupt embryonic muscle patterning. These resources enable high-resolution high-throughput genetic mapping in Drosophila.

  • 6.
    Clausson, Carl-Magnus
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Allalou, Amin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Weibrecht, Irene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mahmoudi, Salah
    Farnebo, Marianne
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Söderberg, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Increasing the dynamic range of in situ PLA2011In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 8, no 11, p. 892-893Article in journal (Refereed)
  • 7. Colwill, Karen
    et al.
    Nilsson, Peter
    KTH, Proteomik.
    Sundberg, Mårten
    KTH, Proteomik.
    Sjöberg, Ronald
    KTH, Proteomik.
    Sivertsson, Åsa
    KTH, Proteomik.
    Schwenk, Jochen M
    KTH, Proteomik.
    Ottosson Takanen, Jenny
    KTH, Proteomik.
    Hober, Sophia
    KTH, Proteomik.
    Uhlén, Mathias
    KTH, Proteomik.
    Gräslund, Susanne
    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.

  • 8.
    Fuller, Franklin D.
    et al.
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Gul, Sheraz
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Chatterjee, Ruchira
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Burgie, E. Sethe
    Washington Univ St Louis, Dept Biol, St Louis, MO USA..
    Young, Iris D.
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Lebrette, Hugo
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden..
    Srinivas, Vivek
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden..
    Brewster, Aaron S.
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Michels-Clark, Tara
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Clinger, Jonathan A.
    Rice Univ, Dept BioSci, Houston, TX USA..
    Andi, Babak
    Natl Synchrotron Light Source II, Brookhaven Natl Lab, Upton, NY USA..
    Ibrahim, Mohamed
    Humboldt Univ, Inst Biol, Berlin, Germany..
    Pastor, Ernest
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    de Lichtenberg, Casper
    Hussein, Rana
    Humboldt Univ, Inst Biol, Berlin, Germany..
    Pollock, Christopher J.
    Penn State Univ, Dept Chem, University Pk, PA USA..
    Zhang, Miao
    Humboldt Univ, Inst Biol, Berlin, Germany..
    Stan, Claudiu A.
    Stanford PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Kroll, Thomas
    SSRL, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Fransson, Thomas
    Stanford PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Weninger, Clemens
    Stanford PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA USA.;LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Kubin, Markus
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Berlin, Germany..
    Aller, Pierre
    Diamond Light Source Ltd, Harwell Sci & Innovat Campus, Didcot, Oxon, England..
    Lassalle, Louise
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Braeuer, Philipp
    Diamond Light Source Ltd, Harwell Sci & Innovat Campus, Didcot, Oxon, England.;Univ Oxford, Dept Biochem, Oxford, England..
    Miller, Mitchell D.
    Rice Univ, Dept BioSci, Houston, TX USA..
    Amin, Muhamed
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.;Zewail City Sci & Technol, Ctr Photon & Smart Mat, Giza, Egypt..
    Koroidov, Sergey
    Umea Univ, Kemiskt Biol Ctr, Inst Kemi, Umea, Sweden.;Stanford PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Roessler, Christian G.
    Natl Synchrotron Light Source II, Brookhaven Natl Lab, Upton, NY USA.;Ventana Med Syst Inc, Tucson, AZ USA..
    Allaire, Marc
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Sierra, Raymond G.
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Docker, Peter T.
    Diamond Light Source Ltd, Harwell Sci & Innovat Campus, Didcot, Oxon, England..
    Glownia, James M.
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Nelson, Silke
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Koglin, Jason E.
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Zhu, Diling
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Chollet, Matthieu
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Song, Sanghoon
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Lemke, Henrik
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA.;Paul Scherrer Inst, SwissFEL, Villigen, Switzerland..
    Liang, Mengning
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Sokaras, Dimosthenis
    SSRL, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Alonso-Mori, Roberto
    LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Zouni, Athina
    Humboldt Univ, Inst Biol, Berlin, Germany..
    Messinger, Johannes
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Umea Univ, Kemiskt Biol Ctr, Inst Kemi, Umea, Sweden..
    Bergmann, Uwe
    Stanford PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Boal, Amie K.
    Penn State Univ, Dept Chem, University Pk, PA USA.;Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA USA..
    Bollinger, J. Martin, Jr.
    Penn State Univ, Dept Chem, University Pk, PA USA.;Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA USA..
    Krebs, Carsten
    Penn State Univ, Dept Chem, University Pk, PA USA.;Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA USA..
    Hoegbom, Martin
    Stanford Univ, Dept Chem, Stanford, CA USA..
    Phillips, George N., Jr.
    Rice Univ, Dept BioSci, Houston, TX USA.;Rice Univ, Dept Chem, Houston, TX USA..
    Vierstra, Richard D.
    Washington Univ St Louis, Dept Biol, St Louis, MO USA..
    Sauter, Nicholas K.
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Orville, Allen M.
    Diamond Light Source Ltd, Harwell Sci & Innovat Campus, Didcot, Oxon, England..
    Kern, Jan
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.;LCLS, SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Yachandra, Vittal K.
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Yano, Junko
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers2017In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 14, no 4, p. 443-+Article in journal (Refereed)
    Abstract [en]

    X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem IIII, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

  • 9. Hattne, Johan
    et al.
    Echols, Nathaniel
    Tran, Rosalie
    Kern, Jan
    Gildea, Richard J
    Brewster, Aaron S
    Alonso-Mori, Roberto
    Glöckner, Carina
    Hellmich, Julia
    Laksmono, Hartawan
    Sierra, Raymond G
    Lassalle-Kaiser, Benedikt
    Lampe, Alyssa
    Han, Guangye
    Gul, Sheraz
    DiFiore, Dörte
    Milathianaki, Despina
    Fry, Alan R
    Miahnahri, Alan
    White, William E
    Schafer, Donald W
    Seibert, M Marvin
    Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA.
    Koglin, Jason E
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Sellberg, Jonas
    Latimer, Matthew J
    Glatzel, Pieter
    Zwart, Petrus H
    Grosse-Kunstleve, Ralf W
    Bogan, Michael J
    Messerschmidt, Marc
    Williams, Garth J
    Boutet, Sébastien
    Messinger, Johannes
    Zouni, Athina
    Yano, Junko
    Bergmann, Uwe
    Yachandra, Vittal K
    Adams, Paul D
    Sauter, Nicholas K
    Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 5, p. 545-548Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

  • 10. He, Mingyue
    et al.
    Stoevesandt, Oda
    Palmer, Elizabeth A.
    Khan, Farid
    Ericsson, Olle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Taussig, Michael J.
    Printing protein arrays from DNA arrays2008In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 5, no 2, p. 175-177Article in journal (Refereed)
    Abstract [en]

    We describe a method, DNA array to protein array (DAPA), which allows the 'printing' of replicate protein arrays directly from a DNA array template using cell-free protein synthesis. At least 20 copies of a protein array can be obtained from a single DNA array. DAPA eliminates the need for separate protein expression, purification and spotting, and also overcomes the problem of long-term functional storage of surface-bound proteins.

  • 11.
    Jarvius, Jonas
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Melin, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Göransson, Jenny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Stenberg, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Fredriksson, Simon
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gonzalez-Rey, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Digital Quantification using Amplified Single-Molecule Detection2006In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 3, no 9, p. 725-727Article in journal (Refereed)
    Abstract [en]

    We describe a scheme for biomolecule enumeration by converting nanometer-scale specific molecular recognition events mediated by rolling-circle amplification to fluorescent micrometer-sized DNA molecules amenable to discrete optical detection. Our amplified single-molecule detection (SMD) approach preserves the discrete nature of the molecular population, allowing multiplex detection and highly precise quantification of molecules over a dynamic range of seven orders of magnitude. We apply the method for sensitive detection and quantification of the bacterial pathogen Vibrio cholerae.

  • 12. Johansson, Linda C
    et al.
    Arnlund, David
    White, Thomas A
    Katona, Gergely
    DePonte, Daniel P
    Weierstall, Uwe
    Doak, R Bruce
    Shoeman, Robert L
    Lomb, Lukas
    Malmerberg, Erik
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Nass, Karol
    Liang, Mengning
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Bozek, John D
    Caleman, Carl
    Coffee, Ryan
    Coppola, Nicola
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y
    Hartmann, Robert
    Hartmann, Andreas
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S
    Kassemeyer, Stephan
    Kimmel, Nils
    Kirian, Richard A
    Maia, Filipe R N C
    Marchesini, Stefano
    Martin, Andrew V
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sierra, Raymond G
    Soltau, Heike
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Struder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wahlgren, Weixiao Y
    Wang, Xiaoyu
    Weidenspointner, Georg
    Wunderer, Cornelia
    Fromme, Petra
    Chapman, Henry N
    Spence, John C H
    Neutze, Richard
    Lipidic phase membrane protein serial femtosecond crystallography2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 3, p. 263-265Article in journal (Refereed)
    Abstract [en]

    X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.

  • 13.
    Ke, Rongqin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Mignardi, Marco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Pacureanu, Alexandra
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Svedlund, Jessica
    Botling, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology.
    Wählby, Carolina
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    In situ sequencing for RNA analysis in preserved tissue and cells2013In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, no 9, p. 857-860Article in journal (Refereed)
    Abstract [en]

    Tissue gene expression profiling is performed on homogenates or on populations of isolated single cells to resolve molecular states of different cell types. In both approaches, histological context is lost. We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved cells and tissue. We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue sections.

  • 14. Koopmann, Rudolf
    et al.
    Cupelli, Karolina
    Redecke, Lars
    Nass, Karol
    DePonte, Daniel P
    White, Thomas A
    Stellato, Francesco
    Rehders, Dirk
    Liang, Mengning
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Boutet, Sebastien
    Bozek, John D
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Doak, R Bruce
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y
    Hartmann, Andreas
    Hartmann, Robert
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S
    Kassemeyer, Stephan
    Kirian, Richard A
    Lomb, Lukas
    Maia, Filipe R N C
    Kimmel, Nils
    Martin, Andrew V
    Messerschmidt, Marc
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shoeman, Robert L
    Sierra, Raymond G
    Soltau, Heike
    Stern, Stephan
    Struder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wang, Xiaoyu
    Weidenspointner, Georg
    Weierstall, Uwe
    Williams, Garth J
    Wunderer, Cornelia B
    Fromme, Petra
    Spence, John C H
    Stehle, Thilo
    Chapman, Henry N
    Betzel, Christian
    Duszenko, Michael
    In vivo protein crystallization opens new routes in structural biology2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 3, p. 259-262Article in journal (Refereed)
    Abstract [en]

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

  • 15.
    Larsson, Chatarina
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Grundberg, Ida
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Söderberg, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    In situ detection and genotyping of individual mRNA molecules2010In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 7, no 5, p. 395-397Article in journal (Refereed)
    Abstract [en]

    Increasing knowledge about the heterogeneity of mRNA expression within cell populations highlights the need to study transcripts at the level of single cells. We present a method for detection and genotyping of individual transcripts based on padlock probes and in situ target-primed rolling-circle amplification. We detect a somatic point mutation, differentiate between members of a gene family and perform multiplex detection of transcripts in human and mouse cells and tissue.

  • 16. Legrand, Delphine
    et al.
    Guillaume, Olivier
    Baguette, Michel
    Cote, Julien
    Trochet, Audrey
    Calvez, Olivier
    Zajitschek, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zajitschek, Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Lecomte, Jane
    Benard, Quentin
    Le Galliard, Jean-Francois
    Clobert, Jean
    The Metatron: an experimental system to study dispersal and metaecosystems for terrestrial organisms2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 8, p. 828-+Article in journal (Refereed)
    Abstract [en]

    Dispersal of organisms generates gene flow between populations. Identifying factors that influence dispersal will help predict how species will cope with rapid environmental change. We developed an innovative infrastructure, the Metatron, composed of 48 interconnected patches, designed for the study of terrestrial organism movement as a model for dispersal. Corridors between patches can be flexibly open or closed. Temperature, humidity and illuminance can be independently controlled within each patch. The modularity and adaptability of the Metatron provide the opportunity for robust experimental design for the study of 'meta-systems'. We describe a pilot experiment on populations of the butterfly Pieris brassicae and the lizard Zootoca vivipara in the Metatron. Both species survived and showed both disperser and resident phenotypes. The Metatron offers the opportunity to test theoretical models in spatial ecology.

  • 17. Mahmutovic, Anel
    et al.
    Fange, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Berg, Otto G
    Elf, Johan
    Lost in presumption: stochastic reactions in spatial models2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105Article in journal (Refereed)
  • 18.
    Mahmutovic, Anel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Fange, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Lost in presumption: stochastic reactions in spatial models2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 12, p. 1163-1166Article in journal (Refereed)
    Abstract [en]

    Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems.

  • 19.
    Maia, Filipe R N C
    NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
    The Coherent X-ray Imaging Data Bank2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 9, p. 854-855Article in journal (Refereed)
  • 20.
    Persson, Fredrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Linden, Martin
    Unoson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Extracting intracellular diffusive states and transition rates from single-molecule tracking data2013In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, no 3, p. 265-269Article in journal (Refereed)
    Abstract [en]

    We provide an analytical tool based on a variational Bayesian treatment of hidden Markov models to combine the information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. The method identifies the number of diffusive states and the state transition rates. Using this method we have created an objective interaction map for Hfq, a protein that mediates interactions between small regulatory RNAs and their mRNA targets.

  • 21.
    Schallmeiner, Edith
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Oksanen, Elli
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Ericsson, Olle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Spångberg, Lena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Eriksson, Susann
    Stenman, Ulf-Håkan
    Pettersson, Kim
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Sensitive protein detection via triple-binder proximity ligation assays2007In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 4, no 2, p. 135-137Article in journal (Refereed)
    Abstract [en]

    The detection of weakly expressed proteins and protein complexes in biological samples represents a fundamental challenge. We have developed a new proximity-ligation strategy named 3PLA that uses three recognition events for the highly specific and sensitive detection of as little as a hundred molecules of the vascular endothelial growth factor (VEGF), the biomarkers troponin I, and prostate-specific antigen (PSA) alone or in complex with an inhibitor--demonstrating the versatility of 3PLA.

  • 22. Shaw, Alan
    et al.
    Lundin, Vanessa
    Petrova, Ekaterina
    Fordos, Ferenc
    Benson, Erik
    Al-Amin, Abdullah
    Herland, Anna
    Blokzijl, Andries
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Högberg, Björn
    Teixeira, Ana I.
    Spatial control of membrane receptor function using ligand nanocalipers2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 8, p. 841-846Article in journal (Refereed)
    Abstract [en]

    The spatial organization of membrane-bound ligands is thought to regulate receptor-mediated signaling. However, direct regulation of receptor function by nanoscale distribution of ligands has not yet been demonstrated, to our knowledge. We developed rationally designed DNA origami nanostructures modified with ligands at well-defined positions. Using these 'nanocalipers' to present ephrin ligands, we showed that the nanoscale spacing of ephrin-A5 directs the levels of EphA2 receptor activation in human breast cancer cells. Furthermore, we found that the nanoscale distribution of ephrin-A5 regulates the invasive properties of breast cancer cells. Our ligand nanocaliper approach has the potential to provide insight into the roles of ligand nanoscale spatial distribution in membrane receptor mediated signaling.

  • 23.
    Söderberg, Ola
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gullberg, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Jarvius, Malin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Ridderstråle, Karin
    Leuchowius, Karl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Jarvius, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Wester, Kenneth
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Hydbring, Per
    Bahram, Fuad
    Larsson, Lars-Gunnar
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Direct observation of individual endogenous protein complexes in situ by proximity ligation2006In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 3, no 12, p. 995-1000Article in journal (Refereed)
    Abstract [en]

    Cellular processes can only be understood as the dynamic interplay of molecules. There is a need for techniques to monitor interactions of endogenous proteins directly in individual cells and tissues to reveal the cellular and molecular architecture and its responses to perturbations. Here we report our adaptation of the recently developed proximity ligation method to examine the subcellular localization of protein-protein interactions at single-molecule resolution. Proximity probes-oligonucleotides attached to antibodies against the two target proteins-guided the formation of circular DNA strands when bound in close proximity. The DNA circles in turn served as templates for localized rolling-circle amplification (RCA), allowing individual interacting pairs of protein molecules to be visualized and counted in human cell lines and clinical specimens. We used this method to show specific regulation of protein-protein interactions between endogenous Myc and Max oncogenic transcription factors in response to interferon-gamma (IFN-gamma) signaling and low-molecular-weight inhibitors.

  • 24. 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
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    van der Maarel, Silvere
    McCafferty, John
    Muyldermans, Serge
    Nygren, Per-Åke
    Palcy, Sandrine
    Plueckthun, Andreas
    Polic, Bojan
    Przybylski, Michael
    Saviranta, Petri
    Sawyer, Alan
    Sherman, David J.
    Skerra, Arne
    Templin, Markus
    Ueffing, Marius
    Uhlén, Mathias
    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.

  • 25. Westenhoff, Sebastian
    et al.
    Malmerberg, Erik
    Arnlund, David
    Johansson, Linda
    Nazarenko, Elena
    Cammarata, Marco
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Chaptal, Vincent
    Abramson, Jeff
    Katona, Gergely
    Menzel, Andreas
    Neutze, Richard
    Rapid readout detector captures protein time-resolved WAXS2010In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 7, no 10, p. 775-776Article in journal (Refereed)
  • 26.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The quest for multiplexed spatially resolved transcriptional profiling2016In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 13, no 8, p. 623-624Article in journal (Other academic)
  • 27.
    Wählby, Carolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kamentsky, Lee
    Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA.
    Liu, Zihan H
    Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA.
    Riklin-Raviv, Tammy
    Conery, Annie L
    Dept. of Molecular Biology and Center for Computational and Integrative Biology, Mass. General Hospital, Boston, MA.
    O'Rourke, Eyleen
    Sokolnicki, Katherine
    Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA.
    Visvikis, Orane
    Developmental Immunology Program, Dept. of Pediatrics, Mass. General Hospital, Boston, MA.
    Ljosa, Vebjorn
    Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA.
    Irazoqui, Javier E
    Developmental Immunology Program, Dept. of Pediatrics, Mass. General Hospital, Boston, MA.
    Golland, Polina
    Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA.
    Ruvkun, Gary
    Ausubel, Frederick M
    Dept. of Molecular Biology and Center for Computational and Integrative Biology, Mass. General Hospital, Boston, MA.
    Carpenter, Anne E
    Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA.
    An image analysis toolbox for high-throughput C. elegans assays2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 7, p. 714-716Article in journal (Refereed)
    Abstract [en]

    We present a toolbox for high-throughput screening of image-based Caenorhabditis elegans phenotypes. The image analysis algorithms measure morphological phenotypes in individual worms and are effective for a variety of assays and imaging systems from different laboratories. The toolbox is available via the open-source CellProfiler project and enables objective scoring of whole-animal high-throughput image-based assays using this unique model organism for the study of diverse biological pathways relevant to human disease.

1 - 27 of 27
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