Evaluated articles

A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model

1. James D Pearce
2. Sara E Simmonds
3. Gita Mahmoudabadi
4. Lakshmi Krishnan
5. Giovanni Palla
6. Ana-Maria Istrate
7. Alexander Tarashansky
8. Benjamin Nelson
9. Omar Valenzuela
10. Donghui Li
11. Stephen R Quake
12. Theofanis Karaletsos

Reviewed by Arcadia Science

Antibody affinity engineering using antibody repertoire data and machine learning

1. Lena Erlach
2. Simon Friedensohn
3. Daniel Neumeier
4. Derek M. Mason
5. Sai T. Reddy

Reviewed by Arcadia Science

Random UV Mutagenesis for the production of Chlorella vulgaris mutants with low chlorophyll content for the food industry

1. Ivan N. Ivanov
2. Jiří Kopecký
3. Karolína Štěrbová
4. Pavel Hrouzek
5. Martin Lukeš
6. Kateřina Bišová
7. Setyo Budi Kurniawan

Reviewed by Arcadia Science

The antifungal and other bioactive properties of the volatilome of Streptomyces scabiei

1. Nudzejma Stulanovic
2. Djulia Bensaada
3. Loïc Belde
4. Delphine Adam
5. Marc Hanikenne
6. Jean-François Focant
7. Pierre-Hugues Stefanuto
8. Sébastien Rigali

Reviewed by Arcadia Science

Eukaryotes’ closest relatives are internally simple syntrophic archaea

1. Hiroyuki Imachi
2. Masaru K. Nobu
3. Shun’ichi Ishii
4. Yuga Hirakata
5. Tetsuro Ikuta
6. Yuta Isaji
7. Makoto Miyata
8. Masayuki Miyazaki
9. Yuki Morono
10. Kazuyoshi Murata
11. Satoshi Nakagawa
12. Miyuki Ogawara
13. Satoshi Okada
14. Yumi Saito
15. Sanae Sakai
16. Shigeru Shimamura
17. Yuhei O. Tahara
18. Yoshihiro Takaki
19. Yoshinori Takano
20. Eiji Tasumi
21. Katsuyuki Uematsu
22. Toshihiro Yoshimura
23. Ken Takai

Reviewed by Arcadia Science

Balancing stability and flexibility when reshaping archaeal membranes

1. Miguel Amaral
2. Felix Frey
3. Xiuyun Jiang
4. Buzz Baum
5. Anđela Šarić

• Curated by eLife

  eLife Assessment

  This fundamental study characterizes the mechanics and stability of bolalipids from archaeal membranes using a minimalist, physics-based computational model. The authors present a robust mesoscale model of bolalipids-containing membranes, systematically evaluating it across diverse membrane configurations. The results are compelling, demonstrating that the incorporation of bolalipids and regular bilayer lipids in archaeal membranes significantly enhances membrane fluidity and structural stability.

Reviewed by eLife, Arcadia Science

Toward De Novo Protein Design from Natural Language

1. Fengyuan Dai
2. Shiyang You
3. Yudian Zhu
4. Yuan Gao
5. Lihao Fu
6. Xibin Zhou
7. Jin Su
8. Chentong Wang
9. Yuliang Fan
10. Xiaoxiao Ma
11. Xianjun Deng
12. Letong Yu
13. Hui Qian
14. Yan He
15. Yitao Ke
16. Chenchen Han
17. Xing Chang
18. Liangzhen Zheng
19. Sheng Wang
20. Yajie Wang
21. Anping Zeng
22. Shunzhi Wang
23. Tong Si
24. Jianming Liu
25. Hongyuan Lu
26. Fajie Yuan

Reviewed by Arcadia Science

Varicose-projection astrocytes: a reactive phenotype associated with neuropathology

1. Caterina Ciani
2. Giulio Pistorio
3. Simona Giancola
4. Marika Mearelli
5. Francesca Emma Mongelli
6. Delaram Forouzeh
7. Luca Mio
8. Paula Ramos-Gonzalez
9. Carlos Matute
10. Ugne Kuliesiute
11. Sari Elena Dötterer
12. Gediminas Luksys
13. Saulius Rocka
14. Urte Neniskyte
15. Marya Ayub
16. Jean-Marie Graïc
17. Francesco Petrelli
18. Alexei Verkhratsky
19. Nunzio Iraci
20. Fabio Cavaliere
21. Carmen Falcone

Reviewed by Arcadia Science

Self-Organizing Neural Networks in Novel Moving Bodies: Anatomical, Behavioral, and Transcriptional Characterization of a Living Construct with a Nervous System

1. Haleh Fotowat
2. Laurie O’Neill
3. Léo Pio-Lopez
4. Megan Sperry
5. Patrick Erickson
6. Tiffany Lin
7. Michael Levin

Reviewed by Arcadia Science

Inferring genotype-phenotype maps using attention models

1. Krishna Rijal
2. Caroline M. Holmes
3. Samantha Petti
4. Gautam Reddy
5. Michael M. Desai
6. Pankaj Mehta

Reviewed by Arcadia Science

Free‐Form Microfluidic Microneedle Array Patches

1. Ian A. Coates
2. Madison M. Driskill
3. Netra U. Rajesh
4. Gabriel Lipkowitz
5. Dan Ilyn
6. Yue Xu
7. Maria T. Dulay
8. Gunilla B. Jacobson
9. John R. Tumbleston
10. Jillian L. Perry
11. Shaomin Tian
12. Joseph M. DeSimone

Reviewed by Arcadia Science

Life as a Function: Why Transformer Architectures Struggle to Gain Genome-Level Foundational Capabilities

1. Hassan Hassan
2. Kyle Puhger
3. Ali Saadat
4. Johannes Mayer
5. Maximilian Sprang

Reviewed by Arcadia Science

Evolution of gene order in prokaryotes is driven primarily by gene gain and loss

1. Shelly Brezner
2. Sofya K. Garushyants
3. Yuri I. Wolf
4. Eugene V. Koonin
5. Sagi Snir

Reviewed by Arcadia Science

The visual system of the longest-living vertebrate, the Greenland shark

1. Lily G. Fogg
2. Emily Tom
3. Maxime Policarpo
4. William Cho
5. Fangyuan Gao
6. Steven F. Grieco
7. Doreen Hii
8. Aaron E. Fawcett
9. Nicolas Boileau
10. Amalie Bech-Poulsen
11. Kirstine F. Steffensen
12. Cherlyn J Ng
13. Peter G. Bushnell
14. John Fleng Steffensen
15. Richard Brill
16. Walter Salzburger
17. Dorota Skowronska-Krawczyk

Reviewed by Arcadia Science

Low-dimensional genotype-fitness mapping across divergent environments suggests a limiting functions model of fitness

1. Olivia M. Ghosh
2. Grant Kinsler
3. Benjamin H. Good
4. Dmitri A. Petrov

Reviewed by Arcadia Science

Evolutionary adaptations of TRPA1 thermosensitivity and skin thermoregulation in vertebrates

1. Gabriel E. Bertolesi
2. Neda Heshami
3. Sarah McFarlane

Reviewed by Arcadia Science

The retinoic acid receptor regulates development of a key evolutionary novelty - the molluscan shell

1. Keisuke Shimizu
2. Paul A. O’Neill
3. Kazuyoshi Endo
4. Tetsuhiro Kudoh

Reviewed by Arcadia Science

Contributions of T helper 9 cells in endometriosis-associated inflammation and lesion growth

1. Alison McCallion
2. Katherine B. Zutautas
3. Danielle J. Sisnett
4. Priyanka Yolmo
5. Harshavardhan Lingegowda
6. Asha K. Ravishanker
7. Dan Vo Hoang
8. Chandrakant Tayade

Reviewed by Arcadia Science

Machine learning-assisted enzyme engineering through ultra-high throughput sorting and large-scale sequence-function data generation

1. Jingyun Zhang
2. Sangeetha Shanmugam
3. Jing Wui Yeoh
4. Dan Zheng
5. Jan Ron Goh
6. Zhangyuan Lin
7. Chueh Loo Poh

Reviewed by Arcadia Science

Dominant contribution of Asgard archaea to eukaryogenesis

1. Victor Tobiasson
2. Jacob Luo
3. Yuri I Wolf
4. Eugene V Koonin

Reviewed by Arcadia Science