Systems Biology

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

Alveolar early progenitors in the aged human lung have increased expression of ACE2 accompanied with genes involved in beta-amyloid clearance: Indication of SARS-CoV-2 also using soluble ACE2 in aged-lungs to enter ACE2-negative cells

1. Virendra K. Chaudhri

Reviewed by ScreenIT

Biophysical modeling of the SARS-CoV-2 viral cycle reveals ideal antiviral targets

1. Brian T. Castle
2. Carissa Dock
3. Mahya Hemmat
4. Susan Kline
5. Christopher Tignanelli
6. Radha Rajasingham
7. David Masopust
8. Paolo Provenzano
9. Ryan Langlois
10. Timothy Schacker
11. Ashley Haase
12. David J. Odde

Reviewed by ScreenIT

Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2

1. Ernesto Estrada

Reviewed by ScreenIT

The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States

1. Pasquale Laise
2. Gideon Bosker
3. Xiaoyun Sun
4. Yao Shen
5. Eugene F. Douglass
6. Charles Karan
7. Ronald B. Realubit
8. Sergey Pampou
9. Andrea Califano
10. Mariano J. Alvarez

Reviewed by ScreenIT