Arcadia Science

Latest preprint reviews

1. Minimal Amino Acid Alphabet for Protein Design

   This article has 6 authors:

   1. Karel Půbal
   2. Kseniia Kushnir
   3. Vojtěch Spiwok
   4. Karolína Loužecká
   5. Vladimír Setnička
   6. Petra Lipovová

   Reviewed by Arcadia Science

2. BOTany Methods: Accessible Automation for Plant Synthetic Biology

   This article has 4 authors:

   1. Moni Qiande
   2. Abigail Lin
   3. Lianna Larson
   4. Cătălin Voiniciuc

   Reviewed by Arcadia Science

3. Quantifying Behavioral Structure and Persistence in Open-Field Assays Using Entropy and Spectral Metrics

   This article has 4 authors:

   1. Sihak Lee
   2. Daniel J. Choi
   3. Soonwook Choi
   4. Zhanyan Fu

   Reviewed by Arcadia Science

4. Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design

   This article has 3 authors:

   1. Jonathan Feldman
   2. Maximilian Brogi
   3. Jeffrey Skolnick

   Reviewed by Arcadia Science

5. Evolutionary adaptation proceeds through a small number of phenotypic modules

   This article has 5 authors:

   1. Mohammad Hossein Donyavi
   2. Reza Ghelich
   3. Kara Schmidlin
   4. Grant Kinsler
   5. Kerry Geiler-Samerotte

   Reviewed by Arcadia Science

6. ESMDisPred: A Structure-Aware CNN-Transformer Architecture for Intrinsically Disordered Protein Prediction

   This article has 4 authors:

   1. Md Wasi Ul Kabir
   2. Ayon Dey
   3. Farzeen Nafees
   4. Md Tamjidul Hoque

   Reviewed by Arcadia Science

7. A Multi-modal LLM for Dynamic Protein-Ligand Interactions and Generative Molecular Design

   This article has 2 authors:

   1. Haoran Jing
   2. Yutong Miao

   Reviewed by Arcadia Science

8. RAG-ESM: Improving pretrained protein language models via sequence retrieval

   This article has 2 authors:

   1. Damiano Sgarbossa
   2. Anne-Florence Bitbol

   Reviewed by Arcadia Science

9. Evolutionary remodeling of non-canonical ORF translation in mammals

   This article has 7 authors:

   1. Yue Chang
   2. Tianyu Lei
   3. Feng Zhou
   4. Jiawen Jiang
   5. Yu Huang
   6. Ziyang Zhu
   7. Hong Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a large, systematically curated catalog of non-canonical open reading frames (ncORFs) in human and mouse by reanalyzing nearly 400 Ribo-seq datasets using a standardized pipeline; the resulting atlas consolidates ncORF annotations across tissues and provides a valuable reference for understanding non-canonical translation and ORF emergence. The main conclusions are supported by consistent data processing and multiple computational measures of translation and conservation. While the pipeline is transparent and robust, several downstream analyses are descriptive, and some evolutionary interpretations remain correlative; dataset heterogeneity, uneven tissue representation, and limited experimental validation also constrain the strength of a subset of the findings. Overall, the evidence is solid, and the resource will be broadly used by the community.

   Reviewed by Arcadia Science, eLife

10. Fluorescence Lifetime Unmixing: A New Workflow for FLIM Live-Cell Imaging

    This article has 9 authors:

    1. Cornelia Wetzker
    2. Marcelo Leomil Zoccoler
    3. Svetlana Iarovenko
    4. Chukwuebuka William Okafornta
    5. Anja Nobst
    6. Hella Hartmann
    7. Thomas Müller-Reichert
    8. Robert Haase
    9. Gunar Fabig

    Reviewed by Arcadia Science