Systems Biology

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease

1. Ricardo Omar Ramirez Flores
2. Jan David Lanzer
3. Daniel Dimitrov
4. Britta Velten
5. Julio Saez-Rodriguez

Reviewed by Review Commons

Homeostasis, injury, and recovery dynamics at multiple scales in a self-organizing mouse intestinal crypt

1. Louis Gall
2. Carrie Duckworth
3. Ferran Jardi
4. Lieve Lammens
5. Aimee Parker
6. Ambra Bianco
7. Holly Kimko
8. David Mark Pritchard
9. Carmen Pin

• Curated by eLife

  eLife assessment

  The authors developed a valuable mathematical model that describes the spatiotemporal dynamics of cells in the intestinal crypt. The proposed model makes an important contribution to the field, allowing a better understanding of the formation and response dynamics of the intestinal crypt through the effective evaluation of health, disease, and treatment conditions. The authors provided solid evidence of the validity of their model and their conclusions, but some minor claims are not properly justified in the current manuscript. This paper is meant for computational biologists and cancer researchers working on oncotherapies for the intestinal epithelium.

Reviewed by eLife

Systems level identification of a matrisome-associated macrophage polarisation state in multi-organ fibrosis

1. John F Ouyang
2. Kunal Mishra
3. Yi Xie
4. Harry Park
5. Kevin Y Huang
6. Enrico Petretto
7. Jacques Behmoaras

• Curated by eLife

  eLife assessment

  This important study deepens our understanding of macrophage phenotypes in pathological contexts and identifies a new macrophage state associated with tissue fibrosis, as well as putative drivers of this cellular state. The authors provide convincing evidence and performed a well-thought-out and thoroughly described computational analysis of single-cell RNA-sequencing data. This work will be of broad interest to the fields of tissue inflammation, fibrosis, macrophage biology, and immunology.

Reviewed by eLife

A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks

1. Song Feng
2. James A. Sanford
3. Thomas Weber
4. Chelsea M. Hutchinson-Bunch
5. Panshak P. Dakup
6. Vanessa L. Paurus
7. Kwame Attah
8. Herbert M. Sauro
9. Wei-Jun Qian
10. H. Steven Wiley

Reviewed by preLights

A new pipeline SPICE identifies novel JUN-IKZF1 composite elements

1. Peng Li
2. Sree Pulugulla
3. Sonali Das
4. Jangsuk Oh
5. Rosanne Spolski
6. Jian-Xin Lin
7. Warren J Leonard

• Curated by eLife

  eLife assessment

  This valuable study presents a screening pipeline (SPICE) for detecting DNA motif spacing preferences between TF partners. SPICE predicts previously known composite elements, but experiments to elucidate the nature of the predicted novel interaction between JUN and IKZF1 are incomplete. These experiments would benefit from more rigorous approaches using other databases to explore additional relevant data. The work will be of broad interest to those involved in dissecting the regulatory logic of mammalian enhancers and promoters.

Reviewed by eLife

Multiomics analyses reveal dynamic bioenergetic pathways and functional remodeling of the heart during intermittent fasting

1. Thiruma V Arumugam
2. Asfa Alli-Shaik
3. Elisa A Liehn
4. Sharmelee Selvaraji
5. Luting Poh
6. Vismitha Rajeev
7. Yoonsuk Cho
8. Yongeun Cho
9. Jongho Kim
10. Joonki Kim
11. Hannah LF Swa
12. David Tan Zhi Hao
13. Chutima Rattanasopa
14. David Yang-Wei Fann
15. David Castano Mayan
16. Gavin Yong-Quan Ng
17. Sang-Ha Baik
18. Karthik Mallilankaraman
19. Mathias Gelderblom
20. Grant R Drummond
21. Christopher G Sobey
22. Brian K Kennedy
23. Roshni R Singaraja
24. Mark P Mattson
25. Dong-Gyu Jo
26. Jayantha Gunaratne

• Curated by eLife

  eLife assessment

  This study provides a useful catalog of the cardiac proteome and transcriptome in response to intermittent fasting. Although mechanistic integration is limited, the technical aspects have been executed in a solid way, and sufficient evidence is provided to support the main conclusions. Future work can build on this study to expand our understanding of the relationship between dietary perturbations and cardiac function.

Reviewed by eLife

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways

1. Agatha Treveil
2. Balazs Bohar
3. Padhmanand Sudhakar
4. Lejla Gul
5. Luca Csabai
6. Marton Olbei
7. Martina Poletti
8. Matthew Madgwick
9. Tahila Andrighetti
10. Isabelle Hautefort
11. Dezso Modos
12. Tamas Korcsmaros

Reviewed by ScreenIT

HiDeF: identifying persistent structures in multiscale ‘omics data

1. Fan Zheng
2. She Zhang
3. Christopher Churas
4. Dexter Pratt
5. Ivet Bahar
6. Trey Ideker

Reviewed by ScreenIT

System Dynamics Modeling of Within-Host Viral Kinetics of Coronavirus (SARS CoV-2)

1. Javier Burgos

Reviewed by ScreenIT

Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection

1. Jun Ding
2. Jose Lugo-Martinez
3. Ye Yuan
4. Jessie Huang
5. Adam J. Hume
6. Ellen L. Suder
7. Elke Mühlberger
8. Darrell N. Kotton
9. Ziv Bar-Joseph

Reviewed by ScreenIT