A5076785466- Genomics and Chromatin Dynamics
- Cell Image Analysis Techniques
- Chromatin Remodeling and Cancer
- Bioinformatics and Genomic Networks
- Cancer Mechanisms and Therapy
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- interferon and immune responses
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- DNA Repair Mechanisms
- S100 Proteins and Annexins
- Nuclear Structure and Function
- Advanced Proteomics Techniques and Applications
- Protein Degradation and Inhibitors
- ATP Synthase and ATPases Research
- Image Processing Techniques and Applications
- Protein Kinase Regulation and GTPase Signaling
- Microtubule and mitosis dynamics
- Cancer-related gene regulation
- Biomedical Text Mining and Ontologies
- Topic Modeling
- Neonatal Respiratory Health Research
- CRISPR and Genetic Engineering
- Advanced Fluorescence Microscopy Techniques
University of Toronto
2023-2024
Institute of Gene Biology
2014-2023
Engelhardt Institute of Molecular Biology
2011-2017
Russian Academy of Sciences
2014-2016
Fluorescence microscopy data describe protein localization patterns at single-cell resolution and have the potential to reveal whole-proteome functional information with remarkable precision. Yet, extracting biologically meaningful representations from cell micrographs remains a major challenge. Existing approaches often fail learn robust noise-invariant features or rely on supervised labels for accurate annotations. We developed PIFiA (Protein Image-based Functional Annotation),...
SUMMARY A long-standing challenge in human regulatory genomics is that transcription factor (TF) DNA-binding motifs are short and degenerate, while the genome large. Motif scans therefore produce many false-positive binding site predictions. By surveying 179 TFs across 25 families using >1,500 cyclic vitro selection experiments with fragmented, naked, unmodified genomic DNA – a method we term GHT-SELEX (Genomic HT-SELEX) find possess much higher sequence specificity than anticipated....
Most of the human genome is thought to be non-functional, and includes large segments often referred as "dark matter" DNA. The also encodes hundreds putative poorly characterized transcription factors (TFs). We determined genomic binding locations 166 uncharacterized TFs in living cells. Nearly half them associated strongly with known regulatory regions such promoters enhancers, at conserved motif matches co-localizing each other. Surprisingly, other dark matter, largely unique sites, via...
SUMMARY We describe an effort (“Codebook”) to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well 61 control TFs. Nearly 5,000 independent experiments across multiple in vitro vivo assays produced motifs for just over half TFs analyzed (177, or 53%), which most are unique a single TF. The data highlight extensive contribution transposable elements TF evolution, both cis trans , identify tens thousands conserved, base-level...
The PBAF subtype of the mammalian chromatin remodeling SWI/SNF complex has wide and diverse functions in transcription regulation development, being both activator repressor. However, a mechanism accounting for such functional diversity remains unclear. Human PHF10/BAF45a subunit plays an important role brain development but not been studied sufficiently. We have shown that PHF10 gene encodes 2 types evolutionarily conserved, ubiquitously expressed isoforms are incorporated into mutually...
The origin recognition complex (ORC) of eukaryotes associates with the replication origins and initiates pre-replication assembly. In literature, there are several reports interaction ORC different RNAs. Here, we demonstrate for first time a direct THSC/TREX-2 mRNA nuclear export complex. was purified from Drosophila embryonic extract found to bind fraction ORC. This occurred via subunits essential viability. Also, associated mRNP, which facilitated by TREX-2. interacted Nxf1 receptor...
The PBAF chromatin-remodeling complexes are multi-protein machines, regulating expression of genes involved in proliferation and differentiation. PHF10 is a subunit the essential for its association with chromatin. Mammalian expressed as four ubiquitous isoforms, which alternatively incorporated complex differ by their influence on transcription target genes. have different domain structure two them (PHF10-S isoforms) lack C-terminal PHD domains, enables phosphorylation CK-1. Here we found...
The Polybromo-associated BAF (BRG1- or BRM-associated factors) (PBAF) chromatin-remodeling complex is essential for transcription in mammalian cells. In this study, we describe a novel variant of the PBAF from differentiated neuronal cells, called dcPBAF, that differs canonical existing proliferating neuroblasts. We adult neurons, specific subunit PBAF, PHF10, replaced by PHF10 isoform lacks N- and C-terminal domains (called PHF10D). addition, dcPBAF does not contain BRD7 subunit. binds...
Abstract Fluorescence microscopy data describe protein localization patterns at single-cell resolution and have the potential to reveal whole-proteome functional information with remarkable precision. Yet, extracting biologically meaningful representations from cell micrographs remains a major challenge. Existing approaches often fail learn robust noise-invariant features or rely on supervised labels for accurate annotations. We developed PIFiA, ( P rotein I mage-based F unct i onal A...
Chromatin remodeling complex PBAF(SWI/SNF) alters the structure of chromatin and controls gene expression. PHF10 is a specific subunit PBAF expressed as four isoforms in mammalian cells. We demonstrated that all are various human cell types different histological origins. All extensively phosphorylated their phosphorylation level depended on type. Phosphorylation occurs while they incorporated complex, therefore may play an essential role regulation complex's function mechanism action.
Protein function is inherently linked to its localization within the cell, and fluorescent microscopy data an indispensable resource for learning representations of proteins. Despite major developments in molecular representation learning, extracting functional information from biological images remains a non-trivial computational task. Current state-of-the-art approaches use autoencoder models learn high-quality features by reconstructing images. However, such methods are prone capturing...
Learning semantically meaningful representations from scientific documents can facilitate academic literature search and improve performance of recommendation systems. Pre-trained language models have been shown to learn rich textual representations, yet they cannot provide powerful document-level for articles. We propose MIReAD, a simple method that learns high-quality papers by fine-tuning transformer model predict the target journal class based on abstract. train MIReAD more than 500,000...