Evaluated articles

Sequence Modeling Is Not Evolutionary Reasoning

1. Yasha Ektefaie
2. Andrew Shen
3. Lavik Jain
4. Maha Farhat
5. Marinka Zitnik

Reviewed by Arcadia Science

Selenium protects Emiliania huxleyi algae from a bacterial pathogen by modulating oxidative stress

1. Roni Beiralas
2. Shira Ben-Asher
3. Einat Segev

Reviewed by Arcadia Science

Micro𝕊plit: Semantic Unmixing of Fluorescent Microscopy Data

1. Ashesh Ashesh
2. Federico Carrara
3. Igor Zubarev
4. Vera Galinova
5. Melisande Croft
6. Melissa Pezzotti
7. Daozheng Gong
8. Francesca Casagrande
9. Elisa Colombo
10. Stefania Giussani
11. Elena Restelli
12. Eugenia Cammarota
13. Juan Manuel Battagliotti
14. Nikolai Klena
15. Moises Di Sante
16. Raghabendra Adhikari
17. Daniel Feliciano
18. Gaia Pigino
19. Elena Taverna
20. Oliver Harschnitz
21. Nicola Maghelli
22. Norbert Scherer
23. Damian Edward Dalle Nogare
24. Joran Deschamps
25. Francesco Pasqualini
26. Florian Jug

Reviewed by Arcadia Science

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation

1. Nihit Aggarwal
2. Johanna Elena Schmitz
3. Lukas Laufer
4. Sven Rahmann
5. Jörn Walter
6. Abdulrahman Salhab

Reviewed by Arcadia Science

A knowledge-based distance metric highlights underperformance of variant effect predictors on gain-of-function missense variants

1. Lukas Gerasimavicius
2. Joseph A. Marsh

Reviewed by Arcadia Science

Cellpose-SAM: superhuman generalization for cellular segmentation

1. Marius Pachitariu
2. Michael Rariden
3. Carsen Stringer

Reviewed by Arcadia Science

Machine Learning and Network Analysis to Predict Hypothetical Protein Functions of Aeromonas hydrophila

1. Harun Pirim
2. Zaidur Rahman
3. Saviz Saei
4. Sangam Gyawali
5. Mohammad Marufuzzaman
6. Nazanin Tajik
7. Hasan Tekedar

Reviewed by Arcadia Science

A miniaturized, high-throughput buffer-centric method for protein solubility screening

1. Adrian Svoboda
2. Marina Molineris
3. Tomáš Pluskal
4. Teo Hebra

Reviewed by Arcadia Science

Borzoi-informed fine mapping improves causal variant prioritization in complex trait GWAS

1. Divyanshi Srivastava
2. Anya Korsakova
3. Qingbo Wang
4. Luong Ruiz
5. Han Yuan
6. David R Kelley

Reviewed by Arcadia Science

Emergence of specific binding and catalysis from a designed generalist binding protein

1. Yuda Chen
2. Sagar Bhattacharya
3. Lena Bergmann
4. Galen J. Correy
5. Sophia K. Tan
6. Kaipeng Hou
7. Justin Biel
8. Lei Lu
9. Ian Bakanas
10. Alexander N. Volkov
11. Ivan V. Korendovych
12. Nicholas F. Polizzi
13. James S. Fraser
14. William F. DeGrado

Reviewed by Arcadia Science

Expanding automated multiconformer ligand modeling to macrocycles and fragments

1. Jessica Flowers
2. Nathaniel Echols
3. Galen J Correy
4. Priyadarshini Jaishankar
5. Takaya Togo
6. Adam R Renslo
7. Henry van den Bedem
8. James S Fraser
9. Stephanie A Wankowicz

• Curated by eLife

  eLife Assessment

  The work presents a valuable extension of qFit-ligand, a computational method for modeling conformational heterogeneity of ligands in X-ray crystallography and cryo-EM density maps. The authors provide solid evidence of improved capabilities through careful validation against the previous version, particularly in expanding ligand sampling within conformational space. Such improvements suggest practical utility for challenging applications, including macrocyclic compound modeling and crystallographic drug fragment screening.

Reviewed by Arcadia Science, eLife

The Phytophthora parasitica effector AVH195 interacts with ATG8, attenuates host autophagy, and promotes biotrophic infection

1. Serena Testi
2. Marie-Line Kuhn
3. Valérie Allasia
4. Pascaline Auroy
5. Fantao Kong
6. Gilles Peltier
7. Sophie Pagnotta
8. Julie Cazareth
9. Harald Keller
10. Franck Panabières

Reviewed by Arcadia Science

Rac1 Selectively Binds a Specific Lamellipodin Isoform via a Noncanonical Helical Interface

1. Tong Gao
2. Pingfeng Zhang
3. Alison M. Kurimchak
4. James S. Duncan
5. Jinhua Wu

Reviewed by Arcadia Science

Positive genetic interactions: high impact, but underrepresented in the literature

1. Mengyi Sun
2. David M. McCandlish

Reviewed by Arcadia Science

Rapid Cell-Free Combinatorial Mutagenesis Workflow Using Small Oligos Suitable for High-Iteration, Active Learning-Guided Protein Engineering

1. Ryan Godin
2. Sepehr Hejazi
3. Bret Lange
4. Basmala Aldamak
5. Nigel F. Reuel

Reviewed by Arcadia Science

A Singapore-centric Fungal Dataset of 518 Cultivated Strains with Visual Phenotypes and Taxonomic Identity

1. Darren Ten Wei Xian
2. Fong Tian Wong
3. Yee Hwee Lim
4. Winston Koh

Reviewed by Arcadia Science

Multivariate Mutual Information based Feature Selection for Predicting Histone Post-Translational Modifications in Epigenetic Datasets

1. V. K. Dhanasekhar
2. Sibi Raj B. Pillai
3. Nithya Ramakrishnan

Reviewed by Arcadia Science

A high-throughput, image-based assay to assess drug sensitivity of Acanthamoeba castellanii cysts

1. Carrie A. Flynn
2. Andrew Harmez
3. Rebecca I. Colón-Ríos
4. William F. Flynn
5. Barbara I. Kazmierczak

Reviewed by Arcadia Science

Cross-species comparative connectomics reveals the evolution of an olfactory circuit

1. Ruairí J.V. Roberts
2. Christoph Giez
3. Serene Dhawan
4. Song Pang
5. Nadine Randel
6. Zhiyuan Lu
7. Hui Gong
8. Léonard Dekens
9. James Di Frisco
10. C. Shan Xu
11. Harald F. Hess
12. Marta Zlatic
13. Albert Cardona
14. Lucia L. Prieto-Godino

Reviewed by Arcadia Science

Induction of Human Pruriceptors from Pluripotent Stem Cells via Transcription Factors

1. Hisato Iriki
2. Ruiqi Hu
3. Xu Li
4. Erdene Baljinnyam
5. Carina Habich
6. Ichiro Imanishi
7. Loan Miller
8. Kavya Chegireddy
9. Laraib Iqbal Malik
10. Daniel Yassky
11. Aaron Ver Heul
12. Kathleen M. Smith
13. Eric R. Goedken
14. Peter Reinhardt
15. Brian S. Kim
16. Samuele G. Marro

Reviewed by Arcadia Science