Bioengineering

Development of antigen-dextramers for detection and evaluation of CAR T cells

1. Rasmus U. W. Friis
2. Maria Ormhøj
3. Cecilie S. Krüger-Jensen
4. Markus Barden
5. Keerthana Ramanathan
6. Mikkel R. Hansen
7. Hinrich Abken
8. Sine R. Hadrup

Reviewed by Arcadia Science

Lab-in-the-loop therapeutic antibody design with deep learning

1. Nathan C. Frey
2. Isidro Hötzel
3. Samuel D. Stanton
4. Ryan Kelly
5. Robert G. Alberstein
6. Emily Makowski
7. Karolis Martinkus
8. Daniel Berenberg
9. Jack Bevers
10. Tyler Bryson
11. Pamela Chan
12. Alicja Czubaty
13. Tamica D’Souza
14. Henri Dwyer
15. Anna Dziewulska
16. James W. Fairman
17. Allen Goodman
18. Jennifer Hofmann
19. Henry Isaacson
20. Aya Ismail
21. Samantha James
22. Taylor Joren
23. Simon Kelow
24. James R. Kiefer
25. Matthieu Kirchmeyer
26. Joseph Kleinhenz
27. James T. Koerber
28. Julien Lafrance-Vanasse
29. Andrew Leaver-Fay
30. Jae Hyeon Lee
31. Edith Lee
32. Donald Lee
33. Wei-Ching Liang
34. Joshua Yao-Yu Lin
35. Sidney Lisanza
36. Andreas Loukas
37. Jan Ludwiczak
38. Sai Pooja Mahajan
39. Omar Mahmood
40. Homa Mohammadi-Peyhani
41. Santrupti Nerli
42. Ji Won Park
43. Jaewoo Park
44. Stephen Ra
45. Sarah Robinson
46. Saeed Saremi
47. Franziska Seeger
48. Imee Sinha
49. Anna M. Sokol
50. Natasa Tagasovska
51. Hao To
52. Edward Wagstaff
53. Amy Wang
54. Andrew M. Watkins
55. Blair Wilson
56. Shuang Wu
57. Karina Zadorozhny
58. John Marioni
59. Aviv Regev
60. Yan Wu
61. Kyunghyun Cho
62. Richard Bonneau
63. Vladimir Gligorijević

Reviewed by Arcadia Science

Mitochondrial adenine base editing of mouse somatic tissues via adeno-associated viral delivery

1. Christian D Mutti
2. Lindsey Van Haute
3. Lucia Luengo-Gutierrez
4. Keira Turner
5. Pedro Silva-Pinheiro
6. Michal Minczuk

• Curated by eLife

  eLife Assessment

  The authors have demonstrated the use of adenine base editors delivered via adeno-associated viruses to introduce edits in the mitochondrial genome. The manuscript describes the methodology well, and the conclusions are convincingly supported by the results. The valuable results highlight the potential of these base editors to model mtDNA variations in somatic tissues in animal models.

Reviewed by eLife

Scaly-Tail Organ Enhances Static Stability during Pel’s Scaly-tailed Flying Squirrels’ Arboreal Locomotion

1. Andrew K. Schulz
2. Mrudul Chellapurath
3. Pranav C. Khandelwal
4. SeyedReza Rezaei
5. Stefan Merker
6. Ardian Jusufi

Reviewed by preLights

Semantical and geometrical protein encoding toward enhanced bioactivity and thermostability

1. Yang Tan
2. Bingxin Zhou
3. Lirong Zheng
4. Guisheng Fan
5. Liang Hong

• Curated by eLife

  eLife Assessment

  ProtSSN is a valuable approach that generates protein embeddings by integrating sequence and structural information, demonstrating improved prediction of mutation effects on thermostability compared to competing models. The evidence supporting the authors' claims is compelling, with well-executed comparisons. This work will be of particular interest to researchers in bioinformatics and structural biology, especially those focused on protein function and stability.

Reviewed by eLife

DyAb: sequence-based antibody design and property prediction in a low-data regime

1. Joshua Yao-Yu Lin
2. Jennifer L. Hofmann
3. Andrew Leaver-Fay
4. Wei-Ching Liang
5. Stefania Vasilaki
6. Edith Lee
7. Pedro O. Pinheiro
8. Natasa Tagasovska
9. James R. Kiefer
10. Yan Wu
11. Franziska Seeger
12. Richard Bonneau
13. Vladimir Gligorijevic
14. Andrew Watkins
15. Kyunghyun Cho
16. Nathan C. Frey

Reviewed by Arcadia Science

Gut-on-Chip Methodology Based on 3D-Printed Molds: A Cost-Effective and Accessible Approach

1. Elise Delannoy
2. Aurélie Burette
3. Sébastien Janel
4. Catherine Daniel
5. Alexandre Grassart

Reviewed by Arcadia Science

Discovery of Expression-Governing Residues in Proteins

1. Fan Jiang
2. Mingchen Li
3. Banghao Wu
4. Liang Zhang
5. Bozitao Zhong
6. Yuanxi Yu
7. Liang Hong

Reviewed by Arcadia Science

AI-enabled alkaline-resistant evolution of protein to apply in mass production

1. Liqi Kang
2. Banghao Wu
3. Bingxin Zhou
4. Pan Tan
5. Yun (Kenneth) Kang
6. Yongzhen Yan
7. Yi Zong
8. Shuang Li
9. Zhuo Liu
10. Liang Hong

• Curated by eLife

  eLife Assessment

  This important work demonstrates the application of Pro-PRIME, a large language model, to engineer VHH antibodies with enhanced stability for extreme industrial environments. The evidence is convincing, showing through two rounds of design and experimental validation that AI-guided approaches can outperform traditional rational design methods. The solid methodology and results establish a foundation for further exploration of LLM-assisted protein engineering.

Reviewed by eLife

Compositional editing of extracellular matrices by CRISPR/Cas9 engineering of human mesenchymal stem cell lines

1. Sujeethkumar Prithiviraj
2. Alejandro Garcia Garcia
3. Karin Linderfalk
4. Bai Yiguang
5. Sonia Ferveur
6. Ludvig Nilsén Falck
7. Agatheeswaran Subramaniam
8. Sofie Mohlin
9. David Hidalgo Gil
10. Steven J Dupard
11. Dimitra Zacharaki
12. Deepak Bushan Raina
13. Paul E Bourgine

• Curated by eLife

  eLife Assessment

  The study presents a potentially valuable approach to genetically modify cells to produce extracellular matrices with altered compositions, termed cell-laid, engineered extracellular matrices (eECM). The evidence supporting the authors' conclusions regarding the utility of eECM for endogenous repair is solid, although there are some disagreements on the chondrogenicity of lyophilized constructs which was viewed as lacking robust evidence for endochondral ossification.

Reviewed by eLife