1. Integrative Analysis of Neuroimaging and Microbiome Data Predicts Cognitive Decline in Parkinson’s Disease

    This article has 3 authors:
    1. Büşranur Delice
    2. Özkan Ufuk Nalbantoğlu
    3. Süleyman Yıldırım

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  2. Predicting the effect of CRISPR-Cas9-based epigenome editing

    This article has 7 authors:
    1. Sanjit Singh Batra
    2. Alan Cabrera
    3. Jeffrey P Spence
    4. Jacob Goell
    5. Selvalakshmi S Anand
    6. Isaac B Hilton
    7. Yun S Song
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents an advance in efforts to use histone post-translational modification (PTM) data to model gene expression and to predict epigenetic editing activity. Such models are broadly useful to the research community, especially ones that can model and predict epigenetic editing activity, which is novel; additionally, the authors have nicely integrated datasets across cell types into their model. The work is mostly solid, but it would be strengthened by performing further comparisons to existing methods that predict gene expression from PTM data and from more comprehensive functional validation of model-predicted epigenome editing outcomes beyond dCas9-p300 based perturbations. This work will be of interest to the epigenetics and computational modeling communities.

    Reviewed by eLife

    This article has 11 evaluationsAppears in 1 listLatest version Latest activity
  3. Deep Learning Reveals Endogenous Sterols as Allosteric Modulators of the GPCR-Gα Interface

    This article has 18 authors:
    1. Sanjay Kumar Mohanty
    2. Aayushi Mittal
    3. Namra
    4. Aakash Gaur
    5. Subhadeep Duari
    6. Saveena Solanki
    7. Anmol Kumar Sharma
    8. Sakshi Arora
    9. Suvendu Kumar
    10. Vishakha Gautam
    11. Nilesh Kumar Dixit
    12. Karthika Subramanian
    13. Tarini Shankar Ghosh
    14. Debarka Sengupta
    15. Shashi Kumar Gupta
    16. Natarajan Arul Murugan
    17. Deepak Sharma
    18. Gaurav Ahuja
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The authors present a computational pipeline for the identification of endogenous allosteric modulators of GPCRs, with experimental validation performed in a yeast system. This approach is valuable for a broad audience, including GPCR structural biologists, molecular pharmacologists, and computational biophysicists. However, the rigor of the computational methods needs to be strengthened to provide stronger evidence for the study's conclusions, which is currently incomplete. The authors should justify their methodological choices and provide greater detail and clarity regarding each computational layer of the pipeline.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  4. Biophysics-based protein language models for protein engineering

    This article has 8 authors:
    1. Sam Gelman
    2. Bryce Johnson
    3. Chase Freschlin
    4. Arnav Sharma
    5. Sameer D’Costa
    6. John Peters
    7. Anthony Gitter
    8. Philip A. Romero

    Reviewed by Arcadia Science

    This article has 16 evaluationsAppears in 1 listLatest version Latest activity
  5. Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells

    This article has 7 authors:
    1. Roozbeh Dehghannasiri
    2. George Henderson
    3. Rob Bierman
    4. Tavor Baharav
    5. Kaitlin Chaung
    6. Peter Wang
    7. Julia Salzman
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a valuable advance for the analysis of gene expression variation at the level of individual cells by introducing a novel reference-free framework that can detect splicing, fusion, editing, immune-receptor diversity and repeated elements in sequencing data. The evidence supporting these claims is solid, with rigorous validation on simulated datasets and extensive analysis of full-length single-cell sequencing data demonstrating improved performance over existing methods. This work will be of particular interest to researchers developing methods for high-resolution transcriptome analysis and to those studying cellular heterogeneity in health and disease.

    Reviewed by eLife, Arcadia Science

    This article has 6 evaluationsAppears in 2 listsLatest version Latest activity
  6. Pathway activation model for personalized prediction of drug synergy

    This article has 18 authors:
    1. Quang Thinh Trac
    2. Yue Huang
    3. Tom Erkers
    4. Päivi Östling
    5. Anna Bohlin
    6. Albin Österroos
    7. Mattias Vesterlund
    8. Rozbeh Jafari
    9. Ioannis Siavelis
    10. Helena Bäckvall
    11. Santeri Kiviluoto
    12. Lukas M Orre
    13. Mattias Rantalainen
    14. Janne Lehtiö
    15. Sören Lehmann
    16. Olli Kallioniemi
    17. Yudi Pawitan
    18. Trung Nghia Vu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study presents a deep learning framework for predicting synergistic drug combinations for cancer treatment in the AstraZeneca-Sanger (AZS) DREAM Challenge dataset. The level of evidence seems solid, although performance on some datasets seems unconvincing and further validation would be required to demonstrate the generalizability of the model and, in turn, its clinical relevance. The reported tool, DIPx, could be of use for personalized drug synergy prediction and exploring the activated pathways related to the effects of drug combinations.

    Reviewed by eLife

    This article has 14 evaluationsAppears in 1 listLatest version Latest activity
  7. Have protein-ligand co-folding methods moved beyond memorisation?

    This article has 4 authors:
    1. Peter Škrinjar
    2. Jérôme Eberhardt
    3. Janani Durairaj
    4. Torsten Schwede

    Reviewed by Arcadia Science

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  8. MorphoNet 2.0: An innovative approach for qualitative assessment and segmentation curation of large-scale 3D time-lapse imaging datasets

    This article has 7 authors:
    1. Benjamin Gallean
    2. Tao Laurent
    3. Kilian Biasuz
    4. Ange Clement
    5. Noura Faraj
    6. Patrick Lemaire
    7. Emmanuel Faure
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This work presents an important technical advancement with the release of MorphoNet 2.0, a user-friendly, standalone platform for 3D+T segmentation and analysis in biological imaging. The authors provide convincing evidence of the tool's capabilities through illustrative use cases, though broader validation against current state-of-the-art tools would strengthen its position. The software's accessibility and versatility make it a resource that will be of value for the bioimaging community, particularly in specialized subfields.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  9. Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures

    This article has 5 authors:
    1. Daniel Osorio
    2. Parastoo Shahrouzi
    3. Xavier Tekpli
    4. Vessela N Kristensen
    5. Marieke L Kuijjer
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The study conducted by Hurtado et al. offers important insights and solid evidence regarding the prediction of drug combinations for cancer treatment. By leveraging disease-specific drug response profiles and single-cell transcriptional signatures, this research not only demonstrates a novel and effective approach to identifying potential drug synergies but it also enhances our understanding of the underlying mechanisms of drug response prediction.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  10. A comprehensive antigen-antibody complex database unlocking insights into interaction interface

    This article has 8 authors:
    1. Yuwei Zhou
    2. Wenwen Liu
    3. Ziru Huang
    4. Yushu Gou
    5. Siqi Liu
    6. Lixu Jiang
    7. Yue Yang
    8. Jian Huang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This useful manuscript provides a newly curated database (termed AACDB) of antibody-antigens structural information, alongside annotations that are either taken and from the PDB, or added de-novo. Sequences, structures, and annotations can be easily downloaded from the AACDB website, speeding up the development of structure-based algorithms and analysis pipelines to characterize antibody-antigen interactions. The methodology presented for this data curation is solid. The curated dataset will be of broad interest and value to researchers interested in antibody-antigen interactions.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
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