Evaluated articles

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

Meta-Research: Positive genetic interactions have greater scientific impact but are under-represented 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

Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures

1. Christopher J Williams
2. Vincent B Chen
3. David C Richardson
4. Jane S Richardson

Reviewed by Arcadia Science

Open-source cell culture automation system with integrated cell counting for passaging microplate cultures

1. Greg Courville
2. Shivanshi Vaid
3. Alexis Toruño
4. Paul Lebel
5. Joana P. Cabrera
6. Preethi Raghavan
7. Axel Jacobsen
8. George Bell
9. Manuel D. Leonetti
10. Rafael Gómez-Sjöberg

Reviewed by Arcadia Science

Optogenetic actin network assembly on lipid bilayer uncovers the network density-dependent functions of actin-binding proteins

1. Kei Yamamoto
2. Makito Miyazaki

Reviewed by Arcadia Science

Learning the Shape of Evolutionary Landscapes: Geometric Deep Learning Reveals Hidden Structure in Phenotype-to-Fitness Maps

1. Manuel Razo-Mejia
2. Madhav Mani
3. Dmitri A. Petrov

Reviewed by Arcadia Science

AI-guided discovery and optimization of antimicrobial peptides through species-aware language model

1. Daehun Bae
2. Minsang Kim
3. Jiwon Seo
4. Hojung Nam

Reviewed by Arcadia Science

Divergent organelle allocation in the evolution of sperm gigantism revealed from subcellular quantification of nematode sperm with electron microscopy

1. Rebecca Schalkowski
2. Asher D Cutter

Reviewed by Arcadia Science