Evaluated articles

Cellular morphology emerges from polygenic, distributed transcriptional variation

1. Seyedezahra Paylakhi
2. Rafael Geurgas
3. Antionette Yasko
4. Robbee Wedow
5. Matthew Tegtmeyer

Reviewed by Arcadia Science

Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes

1. Elisa Gomez-Gil
2. Paolo Guerra
3. Ying Gu
4. Sherman Foo
5. Benedicte Billard
6. Gabor Balogh
7. Maria Peter
8. Snezhana Oliferenko

Reviewed by Arcadia Science

Evaluating Limits of Machine Learning-Assisted Raman Spectroscopy in Classification of Biological Samples

1. Aman Yadav
2. Arlin Birkby
3. Noah Armstrong
4. Assame Arnob
5. Ming-Hsun Chou
6. Alma Fernandez
7. Aart J. Verhoef
8. Zhenhuan Yi
9. Siddhant Gulati
10. Siddhi Kotnis
11. Qing Sun
12. Katy C. Kao
13. Hung-Jen Wu

Reviewed by Arcadia Science

ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa

1. Cyril Malbranke
2. Gionata Paolo Zalaffi
3. Anne-Florence Bitbol

Reviewed by Arcadia Science

Biophysical trade-offs in antibody evolution are resolved by conformation-mediated epistasis

1. Cole R Tharp
2. Claudio Catalano
3. Anthony Khalifeh
4. Sam Ghaffari-Kashani
5. Ruimin Huang
6. Gyunghoon Kang
7. Giovanna Scapin
8. Angela M Phillips

Reviewed by Arcadia Science

An Automated End-to-End Workflow for Production of Secreted Proteins in Transfected Mammalian Cells

1. Pavee Vasnarungruengkul
2. Michael A. Anaya
3. Annie W. Lam
4. Elisa Gonzalez
5. An Zhang
6. Maxine L. Wang
7. Woj M. Wojtowicz
8. Kai Zinn
9. Jost Vielmetter

Reviewed by Arcadia Science

Branched actin constrains endosomal cargo to control sorting and fission

1. Devin Frisby
2. Naava Naslavsky
3. Steve Caplan

Reviewed by Arcadia Science

A toolkit for programmable transcriptional engineering across eukaryotic kingdoms

1. Izaiah J. Ornelas
2. Lauren A. Owens
3. Simon Alamos
4. Niklas F.C. Hummel
5. Mitzi G. Hernández Zamora
6. Ngan T. Phan
7. Rithu K. Pattali
8. Patrick M. Shih
9. James K. Nuñez

Reviewed by Arcadia Science

Cellquant: a vibecoder’s guide to image analysis

1. Abani Neferkara
2. Asif Ali
3. David Pincus

Reviewed by Arcadia Science

Lysosomal Expansion Compartments Mediate Zinc and Copper Homeostasis in Caenorhabditis elegans

1. Joy R. Armendariz
2. Sean Teng
3. Camdyn Rakow
4. Raquel Herrera
5. Samuel Herrera
6. Moshe T. Gordon
7. Si Chen
8. Stefan Vogt
9. Hanwenheng Liu
10. Makena Jarvis
11. Katryna Reese
12. Aidan T. Pezacki
13. Christopher J. Chang
14. Byung-Eun Kim
15. Daniel L. Schneider
16. Adelita D. Mendoza
17. Kerry Kornfeld

Reviewed by Arcadia Science

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