Evaluated articles

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

New insights into the evolution of spider silk proteins illuminated by long-read transcriptomes

1. Kesen Zhu
2. Shiyi Zhou
3. Mo Lyu
4. Jiahao Xiang
5. Shaohan Niu
6. Yongping Huang
7. Lei Gao
8. Anjiang Tan
9. Hui Xiang

• Curated by eLife

  eLife Assessment

  This valuable study by Zhu et al. offers a high-resolution evolutionary framework for spider silk proteins (spidroins) through long-read transcriptomics across a broad phylogenetic range, with theoretical implications for protein family evolution, biomaterials, and silk biology. By identifying putative ancestral spidroin templates in early-diverging spiders, the authors make a significant contribution to understanding genetic innovations underlying silk diversification. The long-read sequencing approach is well-suited to these highly repetitive genes. However, the support is incomplete: key claims regarding direct ancestry between silk protein families, the independent origin of certain silk types, and the co-option of flagelliform spidroins in non-web-building spiders rely on absence-based inferences and indirect phylogenetic reasoning that the data cannot yet fully substantiate, and some gene family assignments overreach the available molecular evidence.

Reviewed by eLife, Arcadia Science

Identifying Evolutionary Relatedness Effects on Diversification from Phylogenies using Neural Networks

1. Tianjian Qin
2. Koen van Benthem
3. Luis Valente
4. Rampal Etienne

Reviewed by Arcadia Science

Stabilizing Plasmodium falciparum Proteins for Small Molecule Drug Discovery

1. Marius Amann
2. Tim Sträßer
3. Oliver Einsle
4. Stefan Günther

Reviewed by Arcadia Science

The use of cross-validation has overestimated the value of genomic selection in plant breeding

1. Daniel E Runcie

Reviewed by Arcadia Science

Explaining how mutations affect AlphaFold predictions

1. Madeleine F. Clore
2. Joseph F. Thole
3. Suchetan Dontha
4. Pramesh Sharma
5. Naomi Greenberg
6. Marie-Paule Strub
7. Mary Starich
8. Davin Jensen
9. Brian F. Volkman
10. Matthew Coudron
11. Lauren L. Porter

Reviewed by Arcadia Science

Evolution tunes functional sub-state interconversion to boost enzyme function

1. Daniel Salamonsen
2. Andrea Pierangelini
3. Karol Buda
4. Daojiong Wang
5. Marc W. van der Kamp
6. Nobuhiko Tokuriki
7. H. Adrian Bunzel
8. Christopher Frohlich

Reviewed by Arcadia Science

Insertion of rare autism variants in synaptic genes induce novel behavioral phenotypes in C. elegans

1. Dustin Haskell
2. William R. Haury
3. Myra Granato
4. Brandon L. Bastien
5. Michael P. Hart

Reviewed by Arcadia Science

WITHDRAWN: Quantifying lipids in human cells using Raman spectroscopy

1. Barbara Orzechowska
2. Anna Nowakowska
3. Anna Pieczara
4. Wiktoria Korona
5. Łukasz Mateuszuk
6. Malgorzata Baranska

Reviewed by Arcadia Science

Evolutionary basis of intermale sexual behavior by multiple pheromone switches in Drosophila

1. Youcef Ouadah
2. Thomas H. Naragon
3. Hayley Smihula
4. Emily L. Behrman
5. Mohammed A. Khallaf
6. Yun Ding
7. David L. Stern
8. Joseph Parker
9. David J. Anderson

Reviewed by Arcadia Science

The primary cilium controls programmed cell death via its proteasome-regulating function

1. Antonia Wiegering
2. Sandra Hägele
3. Stefanie Kuschel
4. Monika Böddeker
5. Christiane Ott
6. Sophie Saunier
7. Tilman Grune
8. Ulrich Rüther
9. Sylvie Schneider-Maunoury
10. Peter Walentek
11. Thorsten Pfirrmann
12. Christoph Gerhardt

Reviewed by Arcadia Science

Scalable insect cell expression and purification screening applied to CRL4-DCAF substrate receptors

1. Angus D. Cowan
2. Stefan Jaekel
3. Alessio Ciulli

Reviewed by Arcadia Science

Two distinct green algal symbionts cohabiting in the Japanese black salamander Hynobius nigrescens

1. Baptiste Genot
2. Swapnil Eishraq Abedin
3. Naoshi Shinozaki
4. Ryan Kerney
5. Shinichiro Maruyama

Reviewed by Arcadia Science

Symbiont diversity and light-organ morphology in Sepiola affinis

1. Clotilde Bongrand
2. Raphael Lami
3. Marcelino T. Suzuki
4. Eric J. Koch

Reviewed by Arcadia Science

Insecticide alters the evolution of glyphosate resistance in Ipomoea purpurea

1. Grace M. Zhang
2. Regina S. Baucom

Reviewed by Arcadia Science

Generative AI-based design of hybrid transcriptional activator proteins with new DNA-binding specificity

1. Sota L Okuda
2. Atsushi Minami
3. Michio Aiko
4. Kohei Uetsuka
5. Kazuteru Miyazaki
6. Kazumasa Ohtake
7. Daisuke Kiga

Reviewed by Arcadia Science

Beyond one-size-fits-all: single-cell transcriptomic signatures predict drug efficacy and reveal responder subgroups in endometriosis

1. Raúl Pérez-Moraga
2. Cemsel Bafligil
3. Sarah Harden
4. Santiago García-Martín
5. María José Jiménez-Santos
6. Ioanna Tiniakou
7. Sophie Ribeiro-Volturo
8. Line Gies
9. María Teresa Pérez Zaballos
10. Cristina Fernández-Molina

Reviewed by Arcadia Science

The phylogenetic context for the origin of a unique purple-green photosymbiosis

1. Sergio A. Muñoz-Gómez
2. Megan E.S. Sørensen
3. Shahed U.A. Shazib
4. Mann Kyoon Shin
5. Thilo Bauer
6. Martin Kreutz
7. Sebastian Hess

Reviewed by Arcadia Science

Ancestral Protein Reconstruction of a membrane trafficking GTPase uncovers unanticipated properties of the ancestral protein and of modern Arf1 GTPases

1. Marine Alves
2. Mandeep Sivia
3. Kristína Záhonová
4. Catherine L. Jackson
5. Joel B. Dacks

Reviewed by Arcadia Science