Evaluated articles

LabOS: The AI-XR Co-Scientist That Sees and Works With Humans

1. Le Cong
2. David Smerkous
3. Xiaotong Wang
4. Di Yin
5. Zaixi Zhang
6. Ruofan Jin
7. Yinkai Wang
8. Michal Gerasimiuk
9. Ravi K. Dinesh
10. Alex Smerkous
11. Lihan Shi
12. Joy Zheng
13. Ian Lam
14. Xuekun Wu
15. Shilong Liu
16. Peishan Li
17. Yi Zhu
18. Ning Zhao
19. Meenal Parakh
20. Simran Serrao
21. Imran A. Mohammad
22. Chao-Yeh Chen
23. Xiufeng Xie
24. Tiffany Chen
25. David Weinstein
26. Greg Barbone
27. Belgin Caglar
28. John B. Sunwoo
29. Fuxin Li
30. Jia Deng
31. Joseph C. Wu
32. Sanfeng Wu
33. Mengdi Wang

Reviewed by Arcadia Science

Minimal Amino Acid Alphabet for Protein Design

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

Reviewed by Arcadia Science

BOTany Methods: Accessible Automation for Plant Synthetic Biology

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

Reviewed by Arcadia Science

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

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

Reviewed by Arcadia Science

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

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

Reviewed by Arcadia Science

Evolutionary adaptation proceeds through a small number of phenotypic modules

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

Reviewed by Arcadia Science

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

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

Reviewed by Arcadia Science

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

1. Haoran Jing
2. Yutong Miao

Reviewed by Arcadia Science

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

1. Damiano Sgarbossa
2. Anne-Florence Bitbol

Reviewed by Arcadia Science

Evolutionary remodeling of non-canonical ORF translation in mammals

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

• 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

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

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

Exopolysaccharides of Lactobacillus crispatus mediate key balancing interactions with the vaginal mucosa

1. Vanessa Croatti
2. Caroline Dricot
3. Tom Eilers
4. Jelle Dillen
5. Tim Van Rillaer
6. Eline Cauwenberghs
7. Ilke Van Tente
8. Sam Bakelants
9. Dieter Vandenheuvel
10. Camille Allonsius
11. Isabel Pintelon
12. Sofie Thys
13. Wendy Mensah
14. Marina Naldi
15. Peter A. Bron
16. Stijn Wittouck
17. Irina Spacova
18. Carola Parolin
19. Beatrice Vitali
20. Sarah Lebeer

Reviewed by Arcadia Science

Atf6 ^-/- mouse photoreceptors exhibit novel ciliary rootlet defect

1. Allyssa Bradley
2. Kristen Haggerty
3. Eun-Jin Lee
4. Michael A. Robichaux
5. Jonathan H. Lin

Reviewed by Arcadia Science

Contrasting evolutionary forces of specialization and admixture underlie the genomic and phenotypic diversity of Yarrowia lipolytica

1. Sergio Izquierdo-Gea
2. Javier Vicente
3. Tomás A. Peña
4. Pablo Villarreal
5. Francisco A. Cubillos
6. Cécile Neuvéglise
7. Jorge Barriuso
8. Ignacio Belda
9. Javier Ruiz

Reviewed by Arcadia Science

Cell cycle-dependent protein dynamics in budding yeast resolved by deconvolution of bulk proteomics

1. Andre Zylstra
2. Mattia Rovetta
3. Silke R. Vedelaar
4. Christian Bleischwitz
5. Julius A. Fülleborn
6. Yulan van Oppen
7. Hugo P. Markus
8. Kerlen T. Korbeld
9. Andreas Milias-Argeitis
10. Katarzyna Buczak
11. Alexander Schmidt
12. Matthias Heinemann

Reviewed by Arcadia Science

Choice of phenotype scale is critical in biobank-based G×E tests

1. Manuela Costantino
2. Renée Fonseca
3. Zhengtong Liu
4. Zhenhong Huang
5. Sriram Sankararaman
6. Iain Mathieson
7. Andy Dahl

Reviewed by Arcadia Science

Optimizing Protein Production in the One-Pot PURE System: Insights into Reaction Composition and Expression Efficiency

1. Yan Zhang
2. Matas Deveikis
3. Yanping Qiu
4. Lovisa Björn
5. Zachary A. Martinez
6. Tsui-Fen Chou
7. Paul S. Freemont
8. Richard M. Murray

Reviewed by Arcadia Science

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

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

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

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

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

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. Crystal Mackall
13. Zinaida Good
14. Jennifer A. Dionne

Reviewed by Arcadia Science