Arcadia Science

Latest preprint reviews

1. RNA foundation models enable generalizable endometriosis disease classification and stable gene-level interpretation

   This article has 14 authors:

   1. Niccolo McConnell
   2. Jennifer Kelly
   3. Ravikanth Tadikonda
   4. Natalia Mulligan
   5. Joao Bettencourt-Silva
   6. Matthew Madgwick
   7. Ritesh Krishna
   8. James Strudwick
   9. Ashley Evans
   10. Stephen Checkley
   11. Anna Paola Carrieri
   12. Michalis Smyrnakis
   13. Charles H Knowles
   14. Laura-Jayne Gardiner

   Reviewed by Arcadia Science

2. Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic Analysis

   This article has 11 authors:

   1. Jinpu Cai
   2. Yuxuan Wang
   3. Yunhao Qiao
   4. Cheng Wang
   5. Ziqi Rong
   6. Luting Zhou
   7. Haoyang Liu
   8. Meng Jiang
   9. Hongbin Shen
   10. Jingyi Jessica Li
   11. Hongyi Xin

   Reviewed by Arcadia Science

3. Dynamic, single-cell monitoring of CAR T cell identity and activation with Raman spectroscopy

   This article has 15 authors:

   1. Ariel Stiber
   2. Boi Quach
   3. Babatunde Ogunlade
   4. Antony Georgiadis
   5. Kai Chang
   6. Yuanwei Li
   7. Patrick Quinn
   8. Haoqing Wang
   9. Kristin C. Y. Tsui
   10. Charm Ang
   11. Elena Sotillo
   12. David B. Miklos
   13. Crystal Mackall
   14. Zinaida Good
   15. Jennifer A. Dionne

   Reviewed by Arcadia Science

4. Tracking Transgenes with Color: RUBY as a Visual Marker in CRISPR-Edited Mutant Plants in Two Triticum Species

   This article has 5 authors:

   1. Rakesh Kumar
   2. Ann Palayur
   3. China Lunde
   4. Ksenia Krasileva
   5. Matthew J Milner

   Reviewed by Arcadia Science

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

   This article has 7 authors:

   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

6. Execution-aware agent harness for accessible and responsible synthetic biology automation

   This article has 22 authors:

   1. Yuan Gao
   2. Lihao Fu
   3. Yujie Liu
   4. Yizhou Luo
   5. Jianzhi Zhang
   6. Wenzhuo Li
   7. Yunquan Lan
   8. Yanjing Wang
   9. Yingyi Li
   10. Han Jiang
   11. Yongcan Chen
   12. Nan (Dorothy) Zhang
   13. Tessa Alexanian
   14. Lucas Boldrini
   15. Xiao Yi
   16. Boyang Li
   17. Hamid Alinejad-Rokny
   18. Teng Wang
   19. Min Yang
   20. Dongzhan Zhou
   21. Chenli Liu
   22. Tong Si

   Reviewed by Arcadia Science

7. Outpacing E. coli : Development of Vibrio natriegens as a Next-Generation Cloning Host

   This article has 11 authors:

   1. Eric Wei
   2. Michael Louie
   3. Emmett Dessimoz
   4. Curtis Orona
   5. Nicholas Smith
   6. Natalie Holste
   7. Michelle Slind
   8. Han Nguyen
   9. Santhosh Anandhan
   10. Santhosh Kallivalappil
   11. Matthew Weinstock

   Reviewed by Arcadia Science

8. Science should be machine-readable

   This article has 3 authors:

   1. A. Sina Booeshaghi
   2. Laura Luebbert
   3. Lior Pachter

   Reviewed by preLights, Arcadia Science

9. New insights into the evolution of spider silk proteins illuminated by long-read transcriptomes

   This article has 9 authors:

   1. Kesen Zhu
   2. Shiyi Zhou
   3. Mo Lyu
   4. Jiahao Xiang
   5. Shaohan Niu
   6. Yongping Huang
   7. Lei Gao
   8. Anjiang Tan
   9. Hui Xiang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study by Zhu et al. offers a high-resolution evolutionary framework for spider silk proteins (spidroins) through long-read transcriptomics across a broad phylogenetic range, with theoretical implications for protein family evolution, biomaterials, and silk biology. By identifying putative ancestral spidroin templates in early-diverging spiders, the authors make a significant contribution to understanding genetic innovations underlying silk diversification. The long-read sequencing approach is well-suited to these highly repetitive genes. However, the support is incomplete: key claims regarding direct ancestry between silk protein families, the independent origin of certain silk types, and the co-option of flagelliform spidroins in non-web-building spiders rely on absence-based inferences and indirect phylogenetic reasoning that the data cannot yet fully substantiate, and some gene family assignments overreach the available molecular evidence.

   Reviewed by eLife, Arcadia Science

10. Identifying Evolutionary Relatedness Effects on Diversification from Phylogenies using Neural Networks

    This article has 4 authors:

    1. Tianjian Qin
    2. Koen van Benthem
    3. Luis Valente
    4. Rampal Etienne

    Reviewed by Arcadia Science