Evaluated articles

Genomic localization bias of secondary metabolite gene clusters and association with histone modifications in Aspergillus

1. Xin Zhang
2. Iseult Leahy
3. Jérȏme Collemare
4. Michael F. Seidl

Reviewed by Arcadia Science

Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits

1. Rachel L. Neve
2. Emily Giedraitis
3. Madeline S. Akbari
4. Shirli Cohen
5. Vanessa V. Phelan

Reviewed by Arcadia Science

Experimental bleaching of photosymbiotic amoeba revealed strain-dependent differences in algal symbiosis ability

1. Daisuke Yamagishi
2. Ryo Onuma
3. Sachihiro Matsunaga
4. Shin-ya Miyagishima
5. Shinichiro Maruyama

Reviewed by Arcadia Science

Amidase and lysozyme dual functions in TseP reveal a new family of chimeric effectors in the type VI secretion system

1. Zeng-Hang Wang
2. Ying An
3. Ting Zhao
4. Tong-Tong Pei
5. Dora Yuping Wang
6. Xiaoye Liang
7. Wenming Qin
8. Tao Dong

• Curated by eLife

  eLife Assessment

  This important study describes how a single effector of the Type Six Secretion System (T6SS) has two distinct functions, which may contribute to bacterial survival and the development of novel antibacterials. The authors utilized various methods in biochemistry, microbiology, and microscopy to produce convincing data supporting their claims about the protein's function; however, they could clarify the implications for non-experts to enhance the accessibility of this work. This manuscript is of interest to those studying T6SS, particularly those interested in effectors and bacterial enzymes.

Reviewed by eLife, Arcadia Science

Structure-aware protein sequence alignment using contrastive learning

1. Ronghui You
2. Yuhao Yi
3. Shanfeng Zhu

Reviewed by Arcadia Science

Inference of gene regulatory networks for overcoming low performance in real-world data

1. Yusuke Hiki
2. Yuta Tokuoka
3. Takahiro G. Yamada
4. Akira Funahashi

Reviewed by Arcadia Science

Protein Set Transformer: A protein-based genome language model to power high diversity viromics

1. Cody Martin
2. Anthony Gitter
3. Karthik Anantharaman

Reviewed by Arcadia Science

Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage

1. Ling S. Loh
2. Kyle A. DeMarr
3. Martina Tsimba
4. Christa Heryanto
5. Alejandro Berrio
6. Nipam H. Patel
7. Arnaud Martin
8. W. Owen McMillan
9. Gregory A. Wray
10. Joseph J. Hanly

Reviewed by Arcadia Science

Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells

1. Srishti U. Sahu
2. Madalena Castro
3. Joseph J. Muldoon
4. Kunica Asija
5. Stacia K. Wyman
6. Netravathi Krishnappa
7. Lorena de Oñate
8. Justin Eyquem
9. David N. Nguyen
10. Ross C. Wilson

Reviewed by Arcadia Science

A Novel HER2 Protein Identification Methodology in Breast Cancer Cells Using Raman Spectroscopy and Raman Imaging: An Analytical Validation Study

1. Halina Abramczyk
2. Jakub Maciej Surmacki
3. Monika Kopeć

Reviewed by Arcadia Science

An Intra-brainstem Circuit for Pain-induced Inhibition of Itch

1. Jagat Narayan Prajapati
2. Devanshi Piyush Shah
3. Arnab Barik

Reviewed by Arcadia Science

Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python

1. Julian Bender
2. Wignand W. D. Mühlhäuser
3. Johannes P. Zimmerman
4. Friedel Drepper
5. Bettina Warscheid

Reviewed by Arcadia Science

Proteome of human glioblastoma and meningioma tissue small extracellular vesicles

1. Huaqi Su
2. Adityas Purnianto
3. Andrew Kaye
4. Andrew Morokoff
5. Katherine j Drummond
6. Stanley Stylli
7. Laura J Vella

Reviewed by Arcadia Science

Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians

1. Thomas D Lewin
2. Isabel Jiah-Yih Liao
3. Yi-Jyun Luo

Reviewed by Arcadia Science

Mapping the human hematopoietic stem and progenitor cell hierarchy through integrated single-cell proteomics and transcriptomics

1. Benjamin Furtwängler
2. Nil Üresin
3. Sabrina Richter
4. Mikkel Bruhn Schuster
5. Despoina Barmpouri
6. Henrietta Holze
7. Anne Wenzel
8. Kirsten Grønbæk
9. Kim Theilgaard-Mönch
10. Fabian J. Theis
11. Erwin M. Schoof
12. Bo T Porse

Reviewed by Arcadia Science

Comprehensive Phenotyping of Extracellular Vesicles in Blood of Healthy Humans – Insights into Cellular Origin and Biological Variability

1. Marija Holcar
2. Ivica Marić
3. Tobias Tertel
4. Katja Goričar
5. Urška Čegovnik Primožič
6. Darko Černe
7. Bernd Giebel
8. Metka Lenassi

Reviewed by Arcadia Science

Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants

1. Caio A Leal-Dutra
2. Joel Vizueta
3. Tobias Baril
4. Pepijn W Kooij
5. Asta Rødsgaard-Jørgensen
6. Benjamin H Conlon
7. Daniel Croll
8. Jonathan Z Shik

Reviewed by Arcadia Science

Addition of Soil Protists Enhances Performance of Agrochemical Seed Treatments

1. Christopher J. Hawxhurst
2. Travis McClure
3. Daniel Kirk
4. Mikhael Shor
5. Daniel J. Gage
6. Leslie M. Shor

Reviewed by Arcadia Science

Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins

1. Valérie de Crécy-Lagard
2. Raquel Dias
3. Nick Sexson
4. Iddo Friedberg
5. Yifeng Yuan
6. Manal A Swairjo

Reviewed by Arcadia Science

GenomeDelta: detecting recent transposable element invasions without repeat library

1. Riccardo Pianezza
2. Anna Haider
3. Robert Kofler

Reviewed by Arcadia Science