Evaluated articles

GutMeta: online microbiome analysis and interactive visualization with build-in curated human gut microbiome database

1. Yiqi Jiang
2. Yanfei Wang
3. Lijia Che
4. Qian Zhou
5. Shuaicheng Li

Reviewed by Arcadia Science

aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow

1. Zoé Pochon
2. Nora Bergfeldt
3. Emrah Kırdök
4. Mário Vicente
5. Thijessen Naidoo
6. Tom van der Valk
7. N. Ezgi Altınışık
8. Maja Krzewińska
9. Love Dalén
10. Anders Götherström
11. Claudio Mirabello
12. Per Unneberg
13. Nikolay Oskolkov

Reviewed by Arcadia Science

Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome

1. Min Wang
2. Lucas J. Osborn
3. Sunit Jain
4. Xiandong Meng
5. Allison Weakley
6. Jia Yan
7. William J. Massey
8. Venkateshwari Varadharajan
9. Anthony Horak
10. Rakhee Banerjee
11. Daniela S. Allende
12. E. Ricky Chan
13. Adeline M. Hajjar
14. Zeneng Wang
15. Alejandra Dimas
16. Aishan Zhao
17. Kazuki Nagashima
18. Alice G. Cheng
19. Steven Higginbottom
20. Stanley L. Hazen
21. J. Mark Brown
22. Michael A. Fischbach

Reviewed by Arcadia Science

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

1. Francesco Cicconardi
2. Edoardo Milanetti
3. Erika C. Pinheiro de Castro
4. Anyi Mazo-Vargas
5. Steven M. Van Belleghem
6. Angelo Alberto Ruggieri
7. Pasi Rastas
8. Joseph Hanly
9. Elizabeth Evans
10. Chris D. Jiggins
11. W. Owen McMillan
12. Riccardo Papa
13. Daniele Di Marino
14. Arnaud Martin
15. Stephen H. Montgomery

Reviewed by Arcadia Science

Molecular mechanisms of tubulogenesis revealed in the sea star hydro-vascular organ

1. Margherita Perillo
2. S. Zachary Swartz
3. Cosmo Pieplow
4. Gary M. Wessel

Reviewed by Arcadia Science

iPHoP: an integrated machine-learning framework to maximize host prediction for metagenome-assembled virus genomes

1. Simon Roux
2. Antonio Pedro Camargo
3. Felipe H. Coutinho
4. Shareef M. Dabdoub
5. Bas E. Dutilh
6. Stephen Nayfach
7. Andrew Tritt

Reviewed by Arcadia Science

Algae drive convergent bacterial community assembly at low dilution frequency

1. Kaumudi H. Prabhakara
2. Seppe Kuehn

Reviewed by Arcadia Science

Precise transcript targeting by CRISPR-Csm complexes

1. David Colognori
2. Marena Trinidad
3. Jennifer A. Doudna

Reviewed by Arcadia Science

A stress-responsive p38 signaling axis in choanoflagellates

1. Florentine U. Rutaganira
2. Maxwell C. Coyle
3. Maria H.T. Nguyen
4. Iliana Hernandez
5. Alex P. Scopton
6. Arvin C. Dar
7. Nicole King

Reviewed by Life Science Editors Foundation, Arcadia Science

Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins

1. Eric B Zheng
2. Li Zhao

• Curated by eLife

  Evaluation Summary:

  By integrating in silico predictions and mass-spectrometry, this manuscript tackles the problem of annotating the currently nameless stretches of genomic sequence that actually code for proteins. The hundreds of protein coding fruit fly genes described here offer new inroads for studying some of the very youngest functional elements in genomes, particularly those that have recently emerged from non-coding DNA sequences. To clarify the biological significance of the present study, the authors should both highlight the genes mostly like to encode functional products and conduct a comparison to published datasets that used different methods to identify such genes in fruit flies.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by Arcadia Science, eLife

Tunnelling nanotube formation is driven by Eps8/IRSp53‐dependent linear actin polymerization

1. J Michael Henderson
2. Nina Ljubojevic
3. Sevan Belian
4. Thibault Chaze
5. Daryl Castaneda
6. Aude Battistella
7. Quentin Giai Gianetto
8. Mariette Matondo
9. Stéphanie Descroix
10. Patricia Bassereau
11. Chiara Zurzolo

Reviewed by Arcadia Science, Review Commons

Mechanical compression induces persistent bacterial growth during bacteriophage predation

1. Guy Mason
2. Enrique R. Rojas

Reviewed by Arcadia Science

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

1. Hirotaka Suetake
2. Tsukasa Fukusato
3. Takeo Igarashi
4. Tazro Ohta

Reviewed by Arcadia Science, GigaScience

Soil protists can actively redistribute beneficial bacteria along Medicago truncatula roots

1. Christopher J. Hawxhurst
2. Jamie L. Micciulla
3. Charles M. Bridges
4. Mikhael Shor
5. Daniel J. Gage
6. Leslie M. Shor

Reviewed by Arcadia Science

AlphaPulldown—a python package for protein–protein interaction screens using AlphaFold-Multimer

1. Dingquan Yu
2. Grzegorz Chojnowski
3. Maria Rosenthal
4. Jan Kosinski

Reviewed by Arcadia Science

Ranking Peptide Binders by Affinity with AlphaFold**

1. Liwei Chang
2. Alberto Perez

Reviewed by Arcadia Science

Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities

1. Christina C. Saak
2. Emily C. Pierce
3. Cong B. Dinh
4. Daniel Portik
5. Richard Hall
6. Meredith Ashby
7. Rachel J. Dutton

Reviewed by Arcadia Science