Evaluated articles

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 valuable study provides a systematically curated atlas of non-canonical open reading frames translated across normal human and mouse tissues by uniformly integrating nearly 400 ribosome-profiling datasets with independent mass-spectrometry evidence for ncORF-encoded peptides. The convincing analyses connect ncORF evolutionary age and coding constraint with translation level, tissue distribution, and co-translation with canonical coding sequences, offering a broad comparative view of how non-canonical translation changes over mammalian evolution. Although the functions of most ncORF-encoded peptides remain unknown, the scale of their detection across tissues, together with their proteomic and evolutionary signatures, suggests that a substantial subset may have biological functions.

Reviewed by eLife, Arcadia Science

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

Ecological specialization and admixture drive the genomic and phenotypic diversity in 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. David B. Miklos
13. Crystal Mackall
14. Zinaida Good
15. Jennifer A. Dionne

Reviewed by Arcadia Science

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

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

Reviewed by Arcadia Science

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

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

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

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

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

Science should be machine-readable

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

Reviewed by preLights, Arcadia Science