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  • Structured Methods for reproducible science

    Detailed and accurate documentation of the reagents, tools and methods is key for reproducible science. We are introducing Structured Methods, our new Materials and Methods format that includes a Reagents and Tools Table and a Methods and Protocols section allowing the authors can describe their methods in a protocol‐like format.

  • A double‐readout method for quantitative mapping of protein–protein interactions in mammalian cells

    See also: N&V by Mikko Taipale

    Philipp Trepte, Erich E Wanker and colleagues 

    A bioluminescence‐based two‐hybrid method provides two quantitative interaction scores, recovers transient associations and monitors the effects of perturbations on interactions.

  • Forces driving the three‐dimensional folding of eukaryotic genomes

    Alvaro Rada‐Iglesias, Frank G Grosveld, Argyris Papantonis

    This Review discusses the biophysical and regulatory forces contributing to higher‐order genome organization and proposes that chromatin conformations are not so much the result of a linear hierarchy, but rather of both converging and conflicting dynamic forces.

  • Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics

    J Javier Díaz‐Mejía, Frederick P Roth and colleagues

    A new method, Barcode Fusion Genetics to Map Genetic Interactions (BFG‐GI) allows generating double mutants and measuring condition‐dependent genetic interactions en masse. 

  • Latest Online
  • Most Read
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  • Open Access
    Article
    Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution
    Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution
    1. Yolanda Schaerli (yolanda.schaerli{at}unil.ch)*,1,2,
    2. Alba Jiménez3,
    3. José M Duarte2,
    4. Ljiljana Mihajlovic1,2,
    5. Julien Renggli4,
    6. Mark Isalan5,6,
    7. James Sharpe3,7,8 and
    8. Andreas Wagner (andreas.wagner{at}ieu.uzh.ch)*,2,9,10
    1. 1Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    2. 2Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
    3. 3Systems Biology Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
    4. 4Independent Researcher, St‐Sulpice, Switzerland
    5. 5Department of Life Sciences, Imperial College London, London, UK
    6. 6Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
    7. 7Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
    8. 8EMBL Barcelona European Molecular Biology Laboratory, Barcelona, Spain
    9. 9The Swiss Institute of Bioinformatics, Lausanne, Switzerland
    10. 10The Santa Fe Institute, Santa Fe, NM, USA
    1. ↵* Corresponding author. Tel: +41 (0) 21 692 56 02; E‐mail: yolanda.schaerli{at}unil.ch
      Corresponding author. Tel: +41 (0) 44 635 61 41; E‐mail: andreas.wagner{at}ieu.uzh.ch

    Analyses in synthetic circuits show that mutations result in distinct novel phenotypes in two circuits that showed the same phenotype before mutation. This constrained phenotypic variation is caused by differences in the circuits’ regulatory mechanisms.

    Synopsis

    Analyses in synthetic circuits show that mutations result in distinct novel phenotypes in two circuits that showed the same phenotype before mutation. This constrained phenotypic variation is caused by differences in the circuits’ regulatory mechanisms.

    • Two synthetic circuits expressed in E. coli that produce the same phenotype, but through different regulatory mechanisms, are used to study the molecular mechanisms underlying constrained phenotypic variation during evolution.

    • The two networks create different spectra of novel phenotypes after mutation.

    • A combination of experimental measurements, mathematical modeling and DNA sequencing shows that the regulatory mechanisms restrict the phenotypic variation that becomes accessible upon mutation.

    • constrained evolution
    • epistasis
    • gene regulatory networks
    • regulatory mechanisms
    • synthetic circuits

    Mol Syst Biol. (2018) 14: e8102

    • Received November 13, 2017.
    • Revision received August 15, 2018.
    • Accepted August 15, 2018.
    • © 2018 The Authors. Published under the terms of the CC BY 4.0 license

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Yolanda Schaerli, Alba Jiménez, José M Duarte, Ljiljana Mihajlovic, Julien Renggli, Mark Isalan, James Sharpe, Andreas Wagner
    Published online 10.09.2018
    • Development & Differentiation
    • Evolution
    • Synthetic Biology & Biotechnology
  • Open Access
    Article
    Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis
    Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis
    1. Lucia Durrieu1,2,6,7,
    2. Daniel Kirrmaier1,3,
    3. Tatjana Schneidt2,
    4. Ilia Kats1,
    5. Sarada Raghavan1,8,
    6. Lars Hufnagel (hufnagel{at}embl.de)*,2,
    7. Timothy E Saunders (dbsste{at}nus.edu.sg)*,2,4,5 and
    8. Michael Knop (m.knop{at}zmbh.uni-heidelberg.de)*,1,3
    1. 1Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ‐ZMBH Alliance, University of Heidelberg, Heidelberg, Germany
    2. 2European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
    3. 3Deutsches Krebsforschungszentrum (DKFZ) DKFZ‐ZMBH Alliance, Heidelberg, Germany
    4. 4Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore
    5. 5Institute of Molecular and Cell Biology, A*Star, Biopolis, Singapore
    6. 6Present Address: Instituto Leloir, Buenos Aires, Argentina
    7. 7Present Address: Departamento de Fisiología, Biología Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
    8. 8Present Address: p53 Laboratory, A*STAR, Singapore
    1. ↵* Corresponding author. Tel: +49 6221 387 8648; E‐mail: hufnagel{at}embl.de
      Corresponding author. Tel: +65 66011552; E‐mail: dbsste{at}nus.edu.sg
      Corresponding author. Tel: +49 6221 54 4213; E‐mail: m.knop{at}zmbh.uni-heidelberg.de

    The dynamics of Bicoid gradient formation are characterized using a tandem fluorescent timer as a protein‐age sensor. These analyses differentiate between proposed models of gradient formation, estimate the underlying kinetic parameters, and explore temporal changes during blastoderm development.

    Synopsis

    The dynamics of Bicoid gradient formation are characterized using a tandem fluorescent timer as a protein‐age sensor. These analyses differentiate between proposed models of gradient formation, estimate the underlying kinetic parameters, and explore temporal changes during blastoderm development.

    • Tandem fluorescent protein timers are used to distinguish between models of morphogen gradient formation.

    • The spatial distribution of protein age provides insights into the underlying kinetics and indicates an effective Bicoid diffusion constant of 3–4 μm2/s.

    • Bicoid protein degradation is likely playing a critical role in forming the Bicoid morphogen gradient and the Bicoid half‐life is estimated to be around 25 min.

    • Drosophila melanogaster
    • embryogenesis
    • fluorescent timers
    • morphogen gradient
    • SPIM

    Mol Syst Biol. (2018) 14: e8355

    • Received April 3, 2018.
    • Revision received August 6, 2018.
    • Accepted August 7, 2018.
    • © 2018 The Authors. Published under the terms of the CC BY 4.0 license

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Lucia Durrieu, Daniel Kirrmaier, Tatjana Schneidt, Ilia Kats, Sarada Raghavan, Lars Hufnagel, Timothy E Saunders, Michael Knop
    Published online 04.09.2018
    • Development & Differentiation
    • Quantitative Biology & Dynamical Systems
  • Open Access
    Article
    Inheritance of OCT4 predetermines fate choice in human embryonic stem cells
    Inheritance of OCT4 predetermines fate choice in human embryonic stem cells
    1. Samuel C Wolff1,
    2. Katarzyna M Kedziora1,
    3. Raluca Dumitru1,
    4. Cierra D Dungee1,
    5. Tarek M Zikry2,
    6. Adriana S Beltran1,
    7. Rachel A Haggerty3,
    8. JrGang Cheng4,
    9. Margaret A Redick1 and
    10. Jeremy E Purvis (jeremy_purvis{at}med.unc.edu)*,1,3,5
    1. 1Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
    2. 2Department of Biostatistics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
    3. 3Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
    4. 4UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
    5. 5Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
    1. ↵*Corresponding author. Tel: +1 919 962 4923; E‐mail: jeremy_purvis{at}med.unc.edu

    Time‐lapse imaging of OCT4 inheritance over multiple cell divisions show that OCT4 levels established before and during daughter cell formation can predict long‐term OCT4 status. These findings imply that the choice between developmental cell fates can be largely determined at the time of cell birth.

    Synopsis

    Time‐lapse imaging of OCT4 inheritance over multiple cell divisions show that OCT4 levels established before and during daughter cell formation can predict long‐term OCT4 status. These findings imply that the choice between developmental cell fates can be largely determined at the time of cell birth.

    • A live‐cell reporter for human OCT4 allows real‐time monitoring of stem cell pluripotency.

    • Single‐cell differences in OCT4 dynamics predict eventual fate decisions.

    • OCT4 expression levels are inherited from mother to daughter cells.

    • OCT4 levels reestablished shortly after cell division predict differences in long‐term cell states.

    • cell fate
    • human embryonic stem cells
    • OCT4
    • pluripotency
    • single‐cell dynamics

    Mol Syst Biol. (2018) 14: e8140

    • Received January 24, 2018.
    • Revision received July 28, 2018.
    • Accepted July 30, 2018.
    • © 2018 The Authors. Published under the terms of the CC BY 4.0 license

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Samuel C Wolff, Katarzyna M Kedziora, Raluca Dumitru, Cierra D Dungee, Tarek M Zikry, Adriana S Beltran, Rachel A Haggerty, JrGang Cheng, Margaret A Redick, Jeremy E Purvis
    Published online 03.09.2018
    • Development & Differentiation
    • Quantitative Biology & Dynamical Systems
    • Stem Cells
  • Open Access
    Article
    Fibroblast state switching orchestrates dermal maturation and wound healing
    Fibroblast state switching orchestrates dermal maturation and wound healing
    1. Emanuel Rognoni1,†,
    2. Angela Oliveira Pisco1,4,†,
    3. Toru Hiratsuka1,
    4. Kalle H Sipilä1,
    5. Julio M Belmonte2,
    6. Seyedeh Atefeh Mobasseri1,
    7. Christina Philippeos1,
    8. Rui Dilão3 and
    9. Fiona M Watt (fiona.watt{at}kcl.ac.uk)*,1
    1. 1Centre for Stem Cells and Regenerative Medicine, King's College London, London, UK
    2. 2Developmental Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    3. 3Nonlinear Dynamics Group, Instituto Superior Técnico, Lisbon, Portugal
    4. 4Present Address: Chan Zuckerberg Biohub, San Francisco, CA, USA
    1. ↵*Corresponding author. Tel: +44 207188 5608; E‐mail: fiona.watt{at}kcl.ac.uk
    1. ↵† These authors contributed equally to this work

    In vivo live imaging of dermal fibroblasts combined with mathematical modeling shows that fibroblast behaviour switching between two distinct states—proliferating and depositing ECM—defines dermal architecture. These findings are relevant for identifying new therapeutic strategies for skin regeneration.

    Synopsis

    In vivo live imaging of dermal fibroblasts combined with mathematical modeling shows that fibroblast behaviour switching between two distinct states—proliferating and depositing ECM—defines dermal architecture. These findings are relevant for identifying new therapeutic strategies for skin regeneration.

    • Tissue‐scale coordination in murine dermis is driven by the interdependence of cell proliferation and ECM deposition.

    • The tissue architecture is set by a negative feedback loop between ECM deposition/remodelling and proliferation.

    • Fibroblast lineages lose segregation with age.

    • Fibroblast migration is the critical discriminator between dermal development and wound healing.

    • dermis development
    • fibroblast states
    • mathematical modelling
    • tissue architecture
    • wound healing

    Mol Syst Biol. (2018) 14: e8174

    • Received December 18, 2017.
    • Revision received August 2, 2018.
    • Accepted August 3, 2018.
    • © 2018 The Authors. Published under the terms of the CC BY 4.0 license

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Emanuel Rognoni, Angela Oliveira Pisco, Toru Hiratsuka, Kalle H Sipilä, Julio M Belmonte, Seyedeh Atefeh Mobasseri, Christina Philippeos, Rui Dilão, Fiona M Watt
    Published online 29.08.2018
    • Development & Differentiation
    • Quantitative Biology & Dynamical Systems
    • Stem Cells
  • Open Access
    Article
    Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases
    Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases
    1. Daniela Michlmayr1,†,
    2. Theodore R Pak2,†,
    3. Adeeb H Rahman2,3,
    4. El‐Ad David Amir2,3,
    5. Eun‐Young Kim4,
    6. Seunghee Kim‐Schulze2,3,
    7. Maria Suprun5,
    8. Michael G Stewart4,
    9. Guajira P Thomas4,
    10. Angel Balmaseda6,
    11. Li Wang2,
    12. Jun Zhu2,
    13. Mayte Suaréz‐Fariñas2,5,
    14. Steven M Wolinsky4,
    15. Andrew Kasarskis2 and
    16. Eva Harris (eharris{at}berkeley.edu)*,1
    1. 1Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
    2. 2Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
    3. 3Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
    4. 4Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
    5. 5Department of Population Health and Science Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
    6. 6Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
    1. ↵*Corresponding author. Tel: +1 510 642 4845; E‐mail: eharris{at}berkeley.edu
    1. ↵† These authors contributed equally to this work.

    This study comprehensively profiles the innate immune response to CHIKV infection in acutely infected Nicaraguan children. We use multiscale analysis of RNA‐seq, CyTOF and Luminex data to dissect the host response to CHIKV in unprecedented depth.

    Synopsis

    This study comprehensively profiles the innate immune response to CHIKV infection in acutely infected Nicaraguan children. We use multiscale analysis of RNA‐seq, CyTOF and Luminex data to dissect the host response to CHIKV in unprecedented depth.

    • CHIKV infection leads to a monocyte‐driven response during the acute phase of infection as shown by CyTOF immunophenotyping and the detection of monocyte‐attracting cytokines by Luminex.

    • The “intermediate” CD14++CD16+ subpopulation and an activated (CD123+, CX3CR1+ and CD141+) CD14+ monocyte subpopulation associate most strongly with the acute phase of infection when compared against all other identified subpopulations of PBMCs by CyTOF.

    • We discover new transcriptomic signatures for differences in acute‐phase viremia, acute‐phase symptom severity, and convalescent‐phase immunogenicity.

    • We create a multiscale network that summarizes the immunological changes across the cellular and gene expression levels and their interactions with various clinical outcomes, and thereby provide a comprehensive characterization of the pediatric host response to CHIKV infection.

    • chikungunya
    • CyTOF
    • immune profiling
    • pediatric
    • RNA‐seq

    Mol Syst Biol. (2018) 14: e7862

    • Received July 3, 2017.
    • Revision received May 31, 2018.
    • Accepted June 29, 2018.
    • © 2018 The Authors. Published under the terms of the CC BY 4.0 license

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Daniela Michlmayr, Theodore R Pak, Adeeb H Rahman, El‐Ad David Amir, Eun‐Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G Stewart, Guajira P Thomas, Angel Balmaseda, Li Wang, Jun Zhu, Mayte Suaréz‐Fariñas, Steven M Wolinsky, Andrew Kasarskis, Eva Harris
    Published online 27.08.2018
    • Genome-Scale & Integrative Biology
    • Microbiology, Virology & Host Pathogen Interaction
    • Molecular Biology of Disease
  • Open Access
    Article
    Single‐cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction
    Single‐cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction
    1. Andrzej J Rzepiela1,3,
    2. Souvik Ghosh1,
    3. Jeremie Breda1,
    4. Arnau Vina‐Vilaseca1,
    5. Afzal P Syed1,
    6. Andreas J Gruber1,
    7. Katja Eschbach2,
    8. Christian Beisel2,
    9. Erik van Nimwegen1 and
    10. Mihaela Zavolan (mihaela.zavolan{at}unibas.ch)*,1
    1. 1Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
    2. 2Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
    3. 3Present Address: Scientific Center for Optical and Electron Microscopy, ETH Zürich, Zürich, Switzerland
    1. ↵*Corresponding author. Tel: +41 61 207 1577; E‐mail: mihaela.zavolan{at}unibas.ch

    A combination of mathematical modeling and RNA‐seq of single cells with variable miRNA expression provides an approach for inferring the parameters describing the response of miRNA targets expressed in their native context, to variations in miRNA levels.

    Synopsis

    A combination of mathematical modeling and RNA‐seq of single cells with variable miRNA expression provides an approach for inferring the parameters describing the response of miRNA targets expressed in their native context, to variations in miRNA levels.

    • Cell lines are developed with doxycycline‐inducible expression of specific miRNAs.

    • Stochastic variation in single‐cell gene expression can be used to infer biochemical parameters of miRNA‐target interaction.

    • The inferred parameters indicate that in this experimental system, endogenous targets are only marginally affected by the expression of a competing RNA.

    • These analyses further reveal that at intermediate expression levels, where targets respond ultrasensitively to the miRNA, the correlation in target expression increases 2–3 fold.

    • ceRNA
    • Michaelis–Menten constant
    • miRNA regulation
    • scRNA‐Seq
    • target down‐regulation

    Mol Syst Biol. (2018) 14: e8266

    • Received February 6, 2018.
    • Revision received July 31, 2018.
    • Accepted August 3, 2018.
    • © 2018 The Authors. Published under the terms of the CC BY 4.0 license

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Andrzej J Rzepiela, Souvik Ghosh, Jeremie Breda, Arnau Vina‐Vilaseca, Afzal P Syed, Andreas J Gruber, Katja Eschbach, Christian Beisel, Erik van Nimwegen, Mihaela Zavolan
    Published online 27.08.2018
    • Quantitative Biology & Dynamical Systems
    • RNA Biology
  • Open Access
    Method
    Proteome‐wide analysis of phospho‐regulated PDZ domain interactions
    Proteome‐wide analysis of phospho‐regulated PDZ domain interactions
    1. Gustav N Sundell1,
    2. Roland Arnold (r.arnold.2{at}bham.ac.uk)*,2,
    3. Muhammad Ali1,
    4. Piangfan Naksukpaiboon2,
    5. Julien Orts3,
    6. Peter Güntert3,4,
    7. Celestine N Chi (chi.celestine{at}imbim.uu.se)*,5 and
    8. Ylva Ivarsson (ylva.ivarsson{at}kemi.uu.se)*,1
    1. 1Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
    2. 2Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
    3. 3Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
    4. 4Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
    5. 5Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    1. ↵* Corresponding author. Tel: +44 7936624996; E‐mail: r.arnold.2{at}bham.ac.uk
      Corresponding author. Tel: +46 18 471 4557; E‐mail: chi.celestine{at}imbim.uu.se
      Corresponding author. Tel: +46 18 471 40 38; E‐mail: ylva.ivarsson{at}kemi.uu.se

    The study presents phosphomimetic proteomic peptide phage display, a novel method for exploring phospho‐regulated motif‐based interactions. Application to PDZ domains reveals a site‐specific phospho‐regulation of PDZ‐mediated interactions as a switching mechanism of interaction selectivity.

    Synopsis

    The study presents phosphomimetic proteomic peptide phage display, a novel method for exploring phospho‐regulated motif‐based interactions. Application to PDZ domains reveals a site‐specific phospho‐regulation of PDZ‐mediated interactions as a switching mechanism of interaction selectivity.

    • Phosphomimetic proteomic peptide‐phage display (ProP‐PD) is a novel method for simultaneously finding motif‐based interaction and identifying phosphorylation switches.

    • Site‐specific Ser/Thr phosphorylation events enable or disable PDZ domain interactions as revealed by phosphomimetic ProP‐PD.

    • The approach can be used to explore potential phospho‐regulation of motif‐based interactions on a large scale.

    • PDZ domain
    • phage display
    • phosphorylation
    • protein–protein interaction
    • Scribble

    Mol Syst Biol. (2018) 14: e8129

    • Received November 29, 2017.
    • Revision received July 24, 2018.
    • Accepted July 24, 2018.
    • © 2018 The Authors. Published under the terms of the CC BY 4.0 license

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Gustav N Sundell, Roland Arnold, Muhammad Ali, Piangfan Naksukpaiboon, Julien Orts, Peter Güntert, Celestine N Chi, Ylva Ivarsson
    Published online 20.08.2018
    • Methods & Resources
    • Post-translational Modifications, Proteolysis & Proteomics
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Methods

Highlights of new methodologies recently published in Molecular Systems Biology:

  • Image‐based phenotype profiling in CRISPR screens
  • Mapping functional missense variants
  • In situ genotyping after phenotyping of a strain library
  • CRISPR/Cas9 screening with unique molecular identifiers
  • Genetic circuit characterization using RNA‐seq
  • Building models from natural language
  • A spectral model for multiplexed optogenetics
  • Deep learning for high‐content microscopy screens

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