Molecular Systems Biology
Papers 1,255
1 page of 126 pages (1,255 results)
#1Daniel A. Anderson (MIT: Massachusetts Institute of Technology)H-Index: 3
#2Christopher A. Voigt (MIT: Massachusetts Institute of Technology)H-Index: 63
Catalytically dead Cas9 (dCas9) is a programmable transcription factor that can be targeted to promoters through the design of small guide RNAs (sgRNAs), where it can function as an activator or repressor. Natural promoters use overlapping binding sites as a mechanism for signal integration, where the binding of one can block, displace, or augment the activity of the other. Here, we implemented this strategy in Escherichia coli using pairs of sgRNAs designed to repress and then derepress transcr...
#1Xiaonan Liu (UH: University of Helsinki)H-Index: 9
#2Sini Huuskonen (UH: University of Helsinki)
Last. Antti Hassinen (UH: University of Helsinki)H-Index: 14
view all 16 authors...
Treatment options for COVID-19, caused by SARS-CoV-2, remain limited. Understanding viral pathogenesis at the molecular level is critical to develop effective therapy. Some recent studies have explored SARS-CoV-2-host interactomes and provided great resources for understanding viral replication. However, host proteins that functionally associate with SARS-CoV-2 are localized in the corresponding subnetwork within the comprehensive human interactome. Therefore, constructing a downstream network i...
Recent advances in genome-wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell-type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, we present a ChIL-based approach for analyzing the diverse cellular dynamics at the tissue level using high-depth epigenomic data. "ChIL for tissues" allows the analysis of a single tissue section and can repro...
#1Marek Ostaszewski (University of Luxembourg)H-Index: 14
#2Anna Niarakis (Université Paris-Saclay)H-Index: 1
Last. Enrico Glaab (University of Luxembourg)H-Index: 23
view all 140 authors...
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many ...
#1Susan E. Hromada (UW: University of Wisconsin-Madison)H-Index: 5
#2Qian Y (UW: University of Wisconsin-Madison)H-Index: 1
Last. Ophelia S. Venturelli (UW: University of Wisconsin-Madison)H-Index: 12
view all 8 authors...
Understanding the principles of colonization resistance of the gut microbiome to the pathogen Clostridioides difficile will enable the design of defined bacterial therapeutics. We investigate the ecological principles of community resistance to C. difficile using a synthetic human gut microbiome. Using a dynamic computational model, we demonstrate that C. difficile receives the largest number and magnitude of incoming negative interactions. Our results show that C. difficile is in a unique class...
#1Mujdat Zeybel (University of Nottingham)H-Index: 2
#2Ozlem Altay (KTH: Royal Institute of Technology)H-Index: 7
Last. Dilek Ural (Koç University)H-Index: 20
view all 18 authors...
Nonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased h...
#1Hongzhong Lu (Chalmers University of Technology)H-Index: 8
#2Feiran Li (Chalmers University of Technology)H-Index: 4
Last. Eduard J. Kerkhoven (Chalmers University of Technology)H-Index: 21
view all 11 authors...
Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards...
#1Victoria GarridoH-Index: 10
Last. Iván Peñuelas (University of Navarra)H-Index: 34
view all 13 authors...
Bacteria present a promising delivery system for treating human diseases. Here, we engineered the genome-reduced human lung pathogen Mycoplasma pneumoniae as a live biotherapeutic to treat biofilm-associated bacterial infections. This strain has a unique genetic code, which hinders gene transfer to most other bacterial genera, and it lacks a cell wall, which allows it to express proteins that target peptidoglycans of pathogenic bacteria. We first determined that removal of the pathogenic factors...
#1Ksenija Radic Shechter (EMBL-EBI: European Bioinformatics Institute)
#2Eleni Kafkia (University of Cambridge)H-Index: 6
Last. Kiran Raosaheb Patil (University of Cambridge)H-Index: 37
view all 11 authors...
Tumor relapse from treatment-resistant cells (minimal residual disease, MRD) underlies most breast cancer-related deaths. Yet, the molecular characteristics defining their malignancy have largely remained elusive. Here, we integrated multi-omics data from a tractable organoid system with a metabolic modeling approach to uncover the metabolic and regulatory idiosyncrasies of the MRD. We find that the resistant cells, despite their non-proliferative phenotype and the absence of oncogenic signaling...
#1Kevin Neil (Université de Sherbrooke)H-Index: 2
#2Nancy Allard (Université de Sherbrooke)H-Index: 4
Last. Sébastien Rodrigue (Université de Sherbrooke)H-Index: 27
view all 7 authors...
Antibiotic resistance threatens our ability to treat infectious diseases, spurring interest in alternative antimicrobial technologies. The use of bacterial conjugation to deliver CRISPR-cas systems programmed to precisely eliminate antibiotic-resistant bacteria represents a promising approach but requires high in situ DNA transfer rates. We have optimized the transfer efficiency of conjugative plasmid TP114 using accelerated laboratory evolution. We hence generated a potent conjugative delivery ...
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