Systems Biology

  1. DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

    1. Yuzhen Liu
    2. Christopher D McGann
    3. Conor P Herlihy
    4. Mary Krebs
    5. Thomas A Perkins
    6. Rose Fields
    7. Conor K Camplisson
    8. David Z Nwizugbo
    9. Qiaoyi Lin
    10. Nicolas J Longhi
    11. Chris Hsu
    12. Shayan C Avanessian
    13. Ashley F Tsue
    14. Evan E Kania
    15. David M Shechner
    16. Brian J Beliveau
    17. Devin K Schweppe

    • Curated by eLife

      eLife Assessment

      This study presents an important new method for probing the DNA and proteins associated with targeted chromatin domains in cells. The authors present solid evidence that the method can map DNA-DNA interactions for individual loci and can detect proteins enriched near repetitive DNA loci or targeted gene clusters. The methodological details of this study will be of particular interest and utility to chromatin biologists.

    Reviewed by eLife

    10 evaluationsAppears in 1 listLatest version Latest activity

  2. Thymic selection of the T cell receptor repertoire is biased toward autoimmunity in females

    1. Hélène Vantomme
    2. Valentin Quiniou
    3. Leslie Adda
    4. Charline Jouannet
    5. Vanessa Mhanna
    6. Céline Albalaa
    7. Pierre Barennes
    8. Nicolas Coatnoan
    9. Vimala Diderot
    10. Johanna Dubois
    11. Gwladys Fourcade
    12. Kenz Le Gouge
    13. Otriv Frédéric Nguekap Tchoumba
    14. Martin Pezous
    15. Paul Stys
    16. Adrien Six
    17. Encarnita Mariotti-Ferrandiz
    18. David Klatzmann

    • Curated by eLife

      eLife Assessment

      This study provides valuable insights into addressing the question of whether the prevalence of autoimmune disease could be driven by sex differences in the T cell receptor (TCR) repertoire, correlating with higher rates of autoimmune disease in females. The authors compared male and female TCR repertoires using bulk RNA sequencing, from sorted thymocyte subpopulations in pediatric and adult human thymuses; however, the analyses provided do not provide sufficient discrimination and incompletely support the central claims regarding sex differences in the TCR repertoire and potential autoimmune bias.

    Reviewed by eLife

    7 evaluationsAppears in 1 listLatest version Latest activity

  3. Metabolic Trans-Omic Analysis Reveals Key Regulatory Disruption of Energy Metabolism in Alzheimer’s Disease

    1. Tomoharu Katayama
    2. Hikaru Sugimoto
    3. Keigo Morita
    4. Hirohisa Watanabe
    5. Shinya Kuroda

    Reviewed by Review Commons

    4 evaluationsAppears in 1 listLatest version Latest activity

  4. Cell painting in activated cells illuminates phenotypic dark space and uncovers novel drug mechanisms of action

    1. Matylda A Zietek
    2. Akshar Lohith
    3. Derfel Terciano
    4. Beverley M Rabbitts
    5. Aswad Khadilkar
    6. John B MacMillan
    7. R Scott Lokey

    Reviewed by Arcadia Science

    3 evaluationsAppears in 1 listLatest version Latest activity

  5. Five-layer systems analysis of Leishmania stage differentiation reveals an essential role for protein degradation in parasite development

    1. Pascale Pescher
    2. Thibaut Douché
    3. Quentin Giai-Gianetto
    4. Karen Druart
    5. Julie Kovarova
    6. Blaise Li
    7. Thomas Cokelaer
    8. K Shanmugha Rajan
    9. Laura Piel
    10. Céline Besse
    11. Anne Boland
    12. Jean-François Deleuze
    13. Mariette Matondo
    14. Michael P. Barrett
    15. Shulamit Michaeli
    16. Gerald F. Späth

    Reviewed by Review Commons

    5 evaluationsAppears in 1 listLatest version Latest activity

  6. Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates

    1. Irene Lamberti
    2. Jeffrey A Chao
    3. Cédric Gobet
    4. Felix Naef

    • Curated by eLife

      eLife Assessment

      This important study provides evidence for dynamic coupling between translation initiation and elongation that can help maintain low ribosome density and translational homeostasis. The authors combine single-molecule imaging with a new approach to analyze mRNA translation kinetics using Bayesian modeling. This work is overall solid and will be of interest to those studying translational regulation.

    Reviewed by eLife

    10 evaluationsAppears in 1 listLatest version Latest activity

  7. Macrophages maintain signaling fidelity in response to ligand mixtures

    1. Xiaolu Guo
    2. Supriya Sen
    3. Julian Gonzalez
    4. Alexander Hoffmann

    Reviewed by Review Commons

    4 evaluationsAppears in 1 listLatest version Latest activity

  8. Identifying and targeting abnormal mitochondrial localization associated with psychosis

    1. Marzieh Haghighi
    2. Donna McPhie
    3. Mohammad Rohban
    4. Erin Weisbart
    5. David J Logan
    6. Kyle W Karhohs
    7. Suzann M Babb
    8. Jessica D Ewald
    9. Johan Fredin Haslum
    10. Beth A Cimini
    11. Shantanu Singh
    12. Bruce M Cohen
    13. Anne E Carpenter

    Reviewed by Review Commons

    4 evaluationsAppears in 1 listLatest version Latest activity

  9. The lipidomic architecture of the mouse brain

    1. Luca Fusar Bassini
    2. Halima Hannah Schede
    3. Laura Capolupo
    4. Leila Haj Abdullah Alieh
    5. Francesca Venturi
    6. Alessandro Valente
    7. Colas Droin
    8. Daniel Trejo Banos
    9. Irina Khven
    10. Ece Z. Asirim
    11. Anita Nasrallah
    12. Irmak Kaysudu
    13. Ekaterina Krymova
    14. Giovanni D'Angelo
    15. Gioele La Manno

    Reviewed by preLights

    1 evaluationAppears in 1 listLatest version Latest activity

  10. Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz

    1. Christina Schmidt
    2. Denes Turei
    3. Dimitrios Prymidis
    4. Macabe Daley
    5. Christian Frezza
    6. Julio Saez-Rodriguez

    Reviewed by Review Commons

    4 evaluationsAppears in 1 listLatest version Latest activity
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