A5101657008- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Insect and Arachnid Ecology and Behavior
- Genetics, Bioinformatics, and Biomedical Research
- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Insect and Pesticide Research
- Plant and animal studies
- Computational Drug Discovery Methods
- Neurobiology and Insect Physiology Research
- RNA modifications and cancer
- Animal Behavior and Reproduction
- Machine Learning in Bioinformatics
- CRISPR and Genetic Engineering
- Nutrition, Genetics, and Disease
- Cancer Genomics and Diagnostics
- Cell Image Analysis Techniques
- Developmental Biology and Gene Regulation
- Epigenetics and DNA Methylation
Georgia Institute of Technology
2022-2025
The Wallace H. Coulter Department of Biomedical Engineering
2022-2025
University of Illinois Urbana-Champaign
2015-2024
Urbana University
2022-2023
Emory University
2023
Illinois College
2019-2023
University of Johannesburg
2015-2022
Center for Genomic Science
2014-2022
All India Institute of Medical Sciences Rishikesh
2022
International University of the Caribbean
2022
Genomics is a Big Data science and going to get much bigger, very soon, but it not known whether the needs of genomics will exceed other domains. Projecting year 2025, we compared with three major generators Data: astronomy, YouTube, Twitter. Our estimates show that "four-headed beast"—it either on par or most demanding domains analyzed here in terms data acquisition, storage, distribution, analysis. We discuss aspects new technologies need be developed rise up meet computational challenges...
The genome of the zebra finch — a songbird and model for study vertebrate brain, behaviour evolution has been sequenced. Its comparison with chicken genome, only other bird available, shows that genes neural function implicated in cognitive processing song have rapidly evolving lineage. also vocal communication engages much brain transcriptome identifies potential integrator microRNA signals linked to communication. studying Comparison are Moreover, brain. is an important organism several...
Aging is characterized by specific alterations in gene expression, but their underlying mechanisms and functional consequences are not well understood. Here we develop a systematic approach to identify combinatorial cis -regulatory motifs that drive age-dependent expression across different tissues organisms. Integrated analysis of 365 microarrays spanning nine tissue types predicted fourteen as major regulators human mouse. The motif most strongly associated with aging was the transcription...
For bees, many roads lead to social harmony Eusociality, where workers sacrifice their reproductive rights support the colony, has evolved repeatedly and represents most form of evolution in insects. Kapheim et al. looked across genomes 10 bee species with varying degrees sociality determine underlying genomic contributions. No one path led eusociality, but similarities were seen features such as increases gene regulation methylation. It also seems that selection pressures relaxed after...
A prominent theory states that animal phenotypes arise by evolutionary changes in gene regulation, but the extent to which this holds true for behavioral evolution is not known. Because “nature and nurture” are now understood involve hereditary environmental influences on expression, we studied whether a phenotype, i.e., aggression, could have evolved into inherited differences via expression. Here, with microarray analysis of honey bees, show aggression-related genes patterns brain...
Abstract Intravital microscopy (IVM) emerged and matured as a powerful tool for elucidating pathways in biological processes. Although label-free multiphoton IVM is attractive its non-perturbative nature, wide application has been hindered, mostly due to the limited contrast of each imaging modality challenge integrate them. Here we introduce simultaneous autofluorescence-multiharmonic (SLAM) microscopy, single-excitation source nonlinear platform that uses custom-designed excitation window...
FlyFactorSurvey (http://pgfe.umassmed.edu/TFDBS/) is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. The provides community access to over 400 recognition motifs and position weight matrices 200 TFs, including many unpublished motifs. Search tools flat file downloads are provided retrieve site information (as sequences, sequence logos) individual groups TFs or all with characterized specificities....
Abstract Motivation: The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. Results: We develop a computational method that uses Hidden Markov Models an Expectation Maximization algorithm to detect such modules, given weight matrices set transcription factors known work together. Two novel features our probabilistic model are: (i) correlations binding sites, be required module activity, are exploited, (ii)...
Abstract Background This paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes regulatory sequences one or more genes, as well their orthologs other species. Results We propose an algorithm that integrates two important aspects a motif's significance – overrepresentation and cross-species conservation into probabilistic score. The allows input orthologous to be related by any user-specified phylogenetic tree. It is based...
Quantitative models of cis-regulatory activity have the potential to improve our mechanistic understanding transcriptional regulation. However, few available today been based on simplistic assumptions about sequences being modeled, or heuristic approximations underlying regulatory mechanisms. We developed a thermodynamics-based model predict gene expression driven by any DNA sequence, as function transcription factor concentrations and their DNA-binding specificities. It uses statistical...
Specificity data for groups of transcription factors (TFs) in a common regulatory network can be used to computationally identify the location cis -regulatory modules genome. The primary limitation this type analysis is paucity specificity that available majority TFs. We describe an omega-based bacterial one-hybrid system provides rapid method characterizing DNA-binding specificities on genome-wide scale. Using system, 35 members Drosophila melanogaster segmentation have been characterized,...
Significance In some cases similar molecular programs (i.e., conserved genes and gene networks) underlie the expression of phenotypic traits that evolve repeatedly across diverse species. We investigated this possibility in context social behavioral response, using a comparative genomics approach for three distantly related species: house mouse ( Mus musculus ), stickleback fish Gasterosteus aculeatus honey bee Apis mellifera ). An experience territory intrusion modulated brain functional...
Abstract Motivation: The similarity of two biological sequences has traditionally been assessed within the well-established framework alignment. Here we focus on task identifying functional relationships between cis-regulatory that are non-orthologous or greatly diverged. ‘Alignment-free’ measures sequence required in this regime. Results: We investigate use a new score for alignment-free comparison, called score. It is based comparing frequencies all fixed-length words sequences. An...
Abstract Large-scale data acquisition and analysis are often required in the successful implementation of design, build, test, learn (DBTL) cycle biosystems design. However, it has long been hindered by experimental cost, variability, biases, missed insights from traditional methods. Here, we report application an integrated robotic system coupled with machine learning algorithms to fully automate DBTL process for As proof concept, have demonstrated its capacity optimizing lycopene...
Pheromones are very important in animal communication. To learn more about the molecular basis of pheromone action, we studied effects a potent honey bee on brain gene expression. Brood (BP) caused changes expression hundreds genes manner consistent with its known behavioral maturation. exposure young bees causes delay transition from working hive to foraging, and found that BP treatment tended upregulate upregulated specialized brood care but downregulate foragers. However, were age...
Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits parallels those mediate human speech. We found ~10% of the avian genome were regulated by singing, and we a striking regional diversity both basal singing-induced programs four key song nuclei zebra finch, songbird. The region-enriched patterns result distinct combinations transcription factors (TFs), their...
A common approach to benchmarking of single-cell transcriptomics tools is generate synthetic datasets that statistically resemble experimental data. However, most existing simulators do not incorporate transcription factor-gene regulatory interactions underlie expression dynamics. Here, we present SERGIO, a simulator gene data models the stochastic nature as well regulation genes by multiple factors according user-provided network. SERGIO can simulate any number cell types in steady state or...
The discovery of molecular relationships from high-dimensional data is a major open problem in bioinformatics. Machine learning and feature attribution models have shown great promise this context but lack causal interpretation. Here, we show that popular model, under certain assumptions, estimates an average quantity reflecting the direct influence one variable on another. We leverage insight to propose precise definition gene regulatory relationship implement new tool, CIMLA...
Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple factors (TFs) regulating common target genes, through direct or indirect mutual interactions. Many individual examples cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism during animal development. Cooperative TF should be manifest genomic sequences as biased arrangements TF-binding sites. Here, we explore the extent and diversity...
Behavior is among the most dynamic animal phenotypes, modulated by a variety of internal and external stimuli. Behavioral differences are associated with large-scale changes in gene expression, but little known about how these regulated. Here we show transcription factor (TF), ultraspiracle (usp; insect homolog Retinoid X Receptor), working complex transcriptional networks, can regulate behavioral plasticity expression. We first that RNAi knockdown USP honey bee abdominal fat bodies delayed...
Cys 2 -His zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks metazoan genomes. As a first step this process, we have characterized DNA-binding specificities 129 sets from Drosophila using bacterial one-hybrid system. This data set contains for at least one encoded ZFP 70 unique genes 23 alternate splice...
Understanding how social experiences are represented in the brain and shape future responses is a major challenge study of behavior. We addressed this problem by studying behavioral, transcriptomic epigenetic to intrusion honey bees. Previous research showed that initial exposure an intruder provokes immediate attack; we now show also leads longer‐term changes behavior response second intruder, with increases probability responding aggressively intensity aggression lasting 2 1 h,...
Despite extensive interest, extracellular vesicle (EV) research remains technically challenging. One of the unexplored gaps in EV has been inability to characterize spatially and functionally heterogeneous populations EVs based on their metabolic profile. In this paper, we utilize intrinsic optical structural contrast demonstrate vivo/in situ characterization a variety unprocessed (pre)clinical samples. With pixel-level segmentation mask provided by deep neural network, individual can be...