Systems Biology

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

1. Yuzhen Liu
2. Christopher D McGann
3. Conor P Herlihy
4. Mary Krebs
5. Thomas A Perkins
6. Rose Fields
7. Conor K Camplisson
8. David Z Nwizugbo
9. Qiaoyi Lin
10. Nicolas J Longhi
11. Chris Hsu
12. Shayan C Avanessian
13. Ashley F Tsue
14. Evan E Kania
15. David M Shechner
16. Brian J Beliveau
17. Devin K Schweppe

• Curated by eLife

  eLife Assessment

  This study presents an important new method for probing the DNA and proteins associated with targeted chromatin domains in cells. The authors present solid evidence that the method can map DNA-DNA interactions for individual loci and can detect proteins enriched near repetitive DNA loci or targeted gene clusters. The methodological details of this study will be of particular interest and utility to chromatin biologists.

Reviewed by eLife

Cell painting in activated cells illuminates phenotypic dark space and uncovers novel drug mechanisms of action

1. Matylda A Zietek
2. Akshar Lohith
3. Derfel Terciano
4. Beverley M Rabbitts
5. Aswad Khadilkar
6. John B MacMillan
7. R Scott Lokey

Reviewed by Arcadia Science

Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates

1. Irene Lamberti
2. Jeffrey A Chao
3. Cédric Gobet
4. Felix Naef

• Curated by eLife

  eLife Assessment

  This important study provides evidence for dynamic coupling between translation initiation and elongation that can help maintain low ribosome density and translational homeostasis. The authors combine single-molecule imaging with a new approach to analyze mRNA translation kinetics using Bayesian modeling. This work is overall solid and will be of interest to those studying translational regulation.

Reviewed by eLife

Macrophages maintain signaling fidelity in response to ligand mixtures

1. Xiaolu Guo
2. Supriya Sen
3. Julian Gonzalez
4. Alexander Hoffmann

Reviewed by Review Commons

Identifying and targeting abnormal mitochondrial localization associated with psychosis

1. Marzieh Haghighi
2. Donna McPhie
3. Mohammad Rohban
4. Erin Weisbart
5. David J Logan
6. Kyle W Karhohs
7. Suzann M Babb
8. Jessica D Ewald
9. Johan Fredin Haslum
10. Caitlin Ravichandran
11. Beth A Cimini
12. Shantanu Singh
13. Bruce M Cohen
14. Anne E Carpenter

Reviewed by Review Commons

The lipidomic architecture of the mouse brain

1. Luca Fusar Bassini
2. Halima Hannah Schede
3. Laura Capolupo
4. Leila Haj Abdullah Alieh
5. Francesca Venturi
6. Alessandro Valente
7. Colas Droin
8. Daniel Trejo Banos
9. Irina Khven
10. Ece Z. Asirim
11. Anita Nasrallah
12. Irmak Kaysudu
13. Ekaterina Krymova
14. Giovanni D'Angelo
15. Gioele La Manno

Reviewed by preLights

Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz

1. Christina Schmidt
2. Denes Turei
3. Dimitrios Prymidis
4. Macabe Daley
5. Christian Frezza
6. Julio Saez-Rodriguez

Reviewed by Review Commons

Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage

1. Zhiwei Huang
2. Songhao Luo
3. Zihao Wang
4. Zhenquan Zhang
5. Benyuan Jiang
6. Qing Nie
7. Jiajun Zhang

• Curated by eLife

  eLife Assessment

  This study presents DeepTX, a valuable methodological tool that integrates mechanistic stochastic models with single-cell RNA sequencing data to infer transcriptional burst kinetics at genome scale. The approach is broadly applicable and of interest to subfields such as systems biology, bioinformatics, and gene regulation. The evidence supporting the findings is solid, with appropriate validation on synthetic data and thoughtful discussion of limitations related to identifiability and model assumptions.

Reviewed by eLife

Ultrasensitive proteomics uncovers nociceptor diversity and novel pain targets

1. Sampurna Chakrabarti
2. Anuar Makhmut
3. Atena Mohammadi
4. Wenhan Luo
5. Lin Wang
6. Gary R. Lewin
7. Fabian Coscia

Reviewed by PREreview

From Noise to Models to Numbers: Evaluating Negative Binomial Models and Parameter Estimations in Single-Cell RNA-seq

1. Yiling Wang
2. Zhanpeng Shu
3. Zhixing Cao
4. Ramon Grima

Reviewed by Review Commons