A5025870213- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Mathematical Biology Tumor Growth
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- Bacterial Genetics and Biotechnology
- Tuberculosis Research and Epidemiology
- Multiple Myeloma Research and Treatments
- Protist diversity and phylogeny
- Glioma Diagnosis and Treatment
- Coral and Marine Ecosystems Studies
- Protein Degradation and Inhibitors
- Mycobacterium research and diagnosis
- Cancer Genomics and Diagnostics
- Histone Deacetylase Inhibitors Research
- Evolution and Genetic Dynamics
- Marine and coastal plant biology
- Marine animal studies overview
- Lipid Membrane Structure and Behavior
- Gut microbiota and health
- Bioinformatics and Genomic Networks
- Viral gastroenteritis research and epidemiology
- PI3K/AKT/mTOR signaling in cancer
Institute for Systems Biology
2013-2025
InSysBio (Russia)
2022-2025
Lawrence Berkeley National Laboratory
2013
Abstract Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data‐driven models that capture the dynamic interplay environment genome‐encoded regulatory programs two types prokaryotes: E scherichia coli (a bacterium) H alobacterium salinarum (an archaeon). The reveal how genome‐wide distributions cis ‐acting gene elements conditional influences transcription factors at each...
The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay environmental cues genome-encoded regulatory programs in Mtb. Analysis EGRIN 2.0 shows how modulation MtrAB two-component signaling system tunes Mtb growth response related microenvironmental cues. Disruption by tunable CRISPR...
Poor prognosis and drug resistance in glioblastoma (GBM) can result from cellular heterogeneity treatment-induced shifts phenotypic states of tumor cells, including dedifferentiation into glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation resists temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, drives recurrence. Through inference transcriptional regulatory networks (TRNs) patient-derived GSCs (PD-GSCs) at single-cell resolution, we...
Climate change has caused drastic declines in corals. As sessile organisms, response to shifting environmental conditions may include changes gene expression, epigenetic modifications, or the microbiome, but as of yet, a common mechanism stress response, alternative splicing (AS), been under-explored Using short-term acute thermal assays, we investigated patterns AS scleractinian coral Acropora cervicornis during and subsequent overnight recovery phase from low (33°C), medium (35°C), high...
Climate change has caused drastic declines in corals. As sessile organisms, corals acclimate to environmental shifts through genome-wide changes gene expression, epigenetic modifications, and alterations microbiome composition. However, alternative splicing (AS), a conserved mechanism of stress response many been under-explored Using short-term acute thermal assays, we investigated patterns AS the scleractinian coral Acropora cervicornis during low (33°C), medium (35°C), high (37°C) heat...
Glioblastoma (GBM) is a heterogeneous tumor made up of cell states that evolve over time. Here, we modeled evolutionary trajectories during standard-of-care treatment using multi-omic single-cell analysis primary sample, corresponding mouse xenografts subjected to standard care therapy, and recurrent at autopsy. We mined the data with SYstems Genetics Network AnaLysis (scSYGNAL) identify network 52 regulators mediate treatment-induced shifts in xenograft tumor-cell were also reflected...
The scale of post-transcriptional regulation and the implications its interplay with other forms in environmental acclimation are underexplored for organisms domain
The ease of generating high-throughput data has enabled investigations into organismal complexity at the systems level through inference networks interactions among various cellular components (genes, RNAs, proteins and metabolites). wider scientific community, however, currently limited access to tools for network inference, visualization analysis because these tasks often require advanced computational knowledge expensive computing resources. We have designed portal...
Abstract Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to lines therapies. Therefore, we not only need ability predict which are at high risk for disease progression but also a means understand mechanisms underlying their risk. Here, report transcriptional regulatory network (TRN) MM inferred from cross-sectional multi-omics data 881 that predicts how 124 chromosomal abnormalities somatic mutations...
ABSTRACT Poor prognosis and drug resistance in glioblastoma (GBM) can result from cellular heterogeneity treatment-induced shifts phenotypic states of tumor cells, including dedifferentiation into glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation resists temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, drives recurrence. Through inference transcriptional regulatory networks (TRNs) patient-derived GSCs (PD-GSCs) at single-cell...
Abstract The success of Mycobacterium tuberculosis (Mtb) is largely due to its ability withstand multiple stresses encountered in the host. Here, we present a data-driven model that captures dynamic interplay environmental cues and genome-encoded regulatory programs Mtb. genome-wide distribution cis -acting gene elements conditional influences transcription factors at those elicit environment-specific responses. Analysis transcriptional responses may be essential for Mtb survive acidic...
ABSTRACT The scale of post-transcriptional regulation and the implications its interplay with other forms on environmental acclimation is underexplored for organisms domain Archaea. Here, we have investigated in extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating transcriptome-wide locations transcript processing sites (TPS) SmAP1 binding, genome-wide antisense RNAs (asRNAs), consequences RNase_2099C knockout differential expression all genes. This integrated analysis...
Abstract Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to their previous therapies. Although therapies exist with diverse mechanisms action, it is not yet clear how differences MM biology across impacts likelihood success for existing those pipeline. Therefore, we only need ability predict which are at high risk disease progression, but also a means understand underlying risk. We hypothesized that...
Abstract Glioblastoma (GBM) is a heterogeneous tumor made up of cell states that evolve over time. Here, we modeled evolutionary trajectories during standard-of-care treatment using multimodal single-cell analysis primary sample, corresponding mouse xenografts subjected to standard care therapy, and recurrent at autopsy. We mined the data with single SYstems Genetics Network AnaLysis (scSYGNAL) identify network 52 regulators mediate treatment-induced shifts in xenograft tumor-cell were also...
Abstract Glioblastoma is a heterogeneous tumor made up of cell states that evolve over time. We modeled evolutionary trajectories during standard-of-care treatment using multimodal single-cell analysis primary sample, corresponding mouse xenografts subjected to standard care therapy, and recurrent at autopsy. mined the data with single SYstems Genetics Network AnaLysis (scSYGNAL) identify network 52 regulators mediate treatment-induced shifts in xenograft tumor-cell were also reflected...