Edward Perkins

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state.

Playing in the mud-using gene expression to assess contaminant effects on sediment dwelling invertebrates.

Dnm1 forms spirals that are structurally tailored to fit mitochondria.

Disruption of nucleocytoplasmic trafficking of cyclin D1 and topoisomerase II by sanguinarine.

Toxicogenomics in regulatory ecotoxicology.

Gene expression profiles in fathead minnow exposed to 2,4-DNT: correlation with toxicity in mammals.

Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine.

Daphnia magna ecotoxicogenomics provides mechanistic insights into metal toxicity.

Comparative neurotoxicity of two energetic compounds, hexanitrohexaazaisowurtzitane and hexahydro-1,3,5-trinitro-1,3,5-triazine, in the earthworm Eisenia fetida.

The N terminus of the herpes simplex virus type 1 triplex protein, VP19C, cannot be detected on the surface of the capsid shell by using an antibody (hemagglutinin) epitope tag.

Structural features of the scaffold interaction domain at the N terminus of the major capsid protein (VP5) of herpes simplex virus type 1.

Subacute toxicity of oral 2,6-dinitrotoluene and 1,3,5-trinitro-1,3,5-triazine (RDX) exposure to the northern bobwhite (Colinus virginianus).

Mitochondrially targeted effects of berberine [Natural Yellow 18, 5,6-dihydro-9,10-dimethoxybenzo(g)-1,3-benzodioxolo(5,6-a) quinolizinium] on K1735-M2 mouse melanoma cells: comparison with direct effects on isolated mitochondrial fractions.

Dielectrophoretic manipulation and real-time electrical detection of single-nanowire bridges in aqueous saline solutions.

Effects of subchronic exposure to 2,6-dinitrotoluene in the northern bobwhite (Colinus virginianus).

Uptake of hexanitrohexaazaisowurtzitane (CL-20) by the earthworm Eisenia fetida through dermal contact.

Toxicogenomic assessment of the population level impacts of contaminants.

Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks.

Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida.

Toxicogenomic analysis provides new insights into molecular mechanisms of the sublethal toxicity of 2,4,6-trinitrotoluene in Eisenia fetida.

Conventional and immunoelectron microscopy of mitochondria.

Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida.

Perturbation of gene expression and steroidogenesis with in vitro exposure of fathead minnow ovaries to ketoconazole.

Interaction between Epsin/Yap180 adaptors and the scaffolds Ede1/Pan1 is required for endocytosis.

Small capsid protein pORF65 is essential for assembly of Kaposi's sarcoma-associated herpesvirus capsids.

Chemoselective nanowire fuses: chemically induced cleavage and electrical detection of carbon nanofiber bridges.

Sanguinarine cytotoxicity on mouse melanoma K1735-M2 cells--nuclear vs. mitochondrial effects.

GOfetcher: a database with complex searching facility for gene ontology.

Gene expression profiling in Daphnia magna part I: concentration-dependent profiles provide support for the No Observed Transcriptional Effect Level.

Gene expression profiling in Daphnia magna, part II: validation of a copper specific gene expression signature with effluent from two copper mines in California.

Batch Blast Extractor: an automated blastx parser application.

ILOOP--a web application for two-channel microarray interwoven loop design.

Self-assembly of Epstein-Barr virus capsids.

Sublethal effects of subacute exposure to RDX (1,3,5-trinitro-1,3,5-triazine) in the northern bobwhite (Colinus virginianus).

Asymmetric enrichment of PIE-1 in the Caenorhabditis elegans zygote mediated by binary counterdiffusion.

Global gene expression in rat brain and liver after oral exposure to the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

Endocrine disrupting chemicals in fish: developing exposure indicators and predictive models of effects based on mechanism of action.

Neurochemical and electrophysiological diagnosis of reversible neurotoxicity in earthworms exposed to sublethal concentrations of CL-20.

RDX and miRNA Expression in B6C3F1 Mice.

Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus).

How does graphene grow? Easy access to well-ordered graphene films.

Biomarker discovery and transcriptomic responses in Daphnia magna exposed to munitions constituents.

Staphylococcal enterotoxin A induces small clusters of HLA-DR1 on B cells.

An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data.

Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen.

I. Effects of a dopamine receptor antagonist on fathead minnow, Pimephales promelas, reproduction.

II: Effects of a dopamine receptor antagonist on fathead minnow dominance behavior and ovarian gene expression in the fathead minnow and zebrafish.

Differentiation of pluripotent stem cells on multiwalled carbon nanotubes.

Supramolecular assemblies formed on an epitaxial graphene superstructure.

Influence of ovarian stage on transcript profiles in fathead minnow (Pimephales promelas) ovary tissue.

From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite.

A novel gene network inference algorithm using predictive minimum description length approach.

Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk.

MEX-5 enrichment in the C. elegans early embryo mediated by differential diffusion.

Dimethylaminopyridine derivatives of lupane triterpenoids are potent disruptors of mitochondrial structure and function.

Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference.

Quail Genomics: a knowledgebase for Northern bobwhite.

Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks.

Reverse engineering adverse outcome pathways.

Investigations of transcript expression in fathead minnow (Pimephales promelas) brain tissue reveal toxicological impacts of RDX exposure.

In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species.

Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus).

Identification and optimization of classifier genes from multi-class earthworm microarray dataset.

Systems biology: leading the revolution in ecotoxicology.

In vitro gene regulatory networks predict in vivo function of liver.

A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT.

Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida.

Analysis of common and specific mechanisms of liver function affected by nitrotoluene compounds.

Predictive minimum description length principle approach to inferring gene regulatory networks.

Downstream bioengineering of ACE chromosomes for incorporation of site-specific recombination cassettes.

Effects of a short-term exposure to the fungicide prochloraz on endocrine function and gene expression in female fathead minnows (Pimephales promelas).

Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics.

Genomic investigation of year-long and multigenerational exposures of fathead minnow to the munitions compound RDX.

Evaluation of natural and nitramine binding energies to 3-D models of the S1S2 domains in the N-methyl-D-aspartate receptor.

Assessment of chemical mixtures and groundwater effects on Daphnia magna transcriptomics.

Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data.

Ecotoxicogenomics to support ecological risk assessment: a case study with bisphenol A in fish.

First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA.

Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction.

RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags.

Gene expression analysis of CL-20-induced reversible neurotoxicity reveals GABA(A) receptors as potential targets in the earthworm Eisenia fetida.

A graphical systems model and tissue-specific functional gene sets to aid transcriptomic analysis of chemical impacts on the female teleost reproductive axis.

CAPRG: sequence assembling pipeline for next generation sequencing of non-model organisms.

Phase I trial of the combination of flavopiridol and imatinib mesylate in patients with Bcr-Abl+ hematological malignancies.

Learning the structure of gene regulatory networks from time series gene expression data.

A systems toxicology approach to elucidate the mechanisms involved in RDX species-specific sensitivity.

Short-term study investigating the estrogenic potency of diethylstilbesterol in the fathead minnow (Pimephales promelas).

State Space Model with hidden variables for reconstruction of gene regulatory networks.

Transfer-free electrical insulation of epitaxial graphene from its metal substrate.

Multiple environmental stressors elicit complex interactive effects in the western fence lizard (Sceloporus occidentalis).

Motif Participation by Genes in E. coli Transcriptional Networks.

Interspecific effects of 4A-DNT (4-amino-2,6-dinitrotoluene) and RDX (1,3,5-trinitro-1,3,5-triazine) in Japanese quail, Northern bobwhite, and Zebra finch.

Delayed myelosuppression with acute exposure to hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and environmental degradation product hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX) in rats.

The mitochondrial fission adaptors Caf4 and Mdv1 are not functionally equivalent.

A phase I trial of vorinostat and alvocidib in patients with relapsed, refractory, or poor prognosis acute leukemia, or refractory anemia with excess blasts-2.

Surface-sensitive conductivity measurement using a micro multi-point probe approach.

Current Perspectives on the Use of Alternative Species in Human Health and Ecological Hazard Assessments.

The good, the bad, and the toxic: approaching hormesis in Daphnia magna exposed to an energetic compound.

Vital imaging of multicellular spheroids.

Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment.

Effects of BDE-209 contaminated sediments on zebrafish development and potential implications to human health.

Using transcriptomic tools to evaluate biological effects across effluent gradients at a diverse set of study sites in Minnesota, USA.

Identification of biomarkers that distinguish chemical contaminants based on gene expression profiles.

Differential effects and potential adverse outcomes of ionic silver and silver nanoparticles in vivo and in vitro.

Integrated approach to explore the mechanisms of aromatase inhibition and recovery in fathead minnows (Pimephales promelas).

Endocrinology: advances through omics and related technologies.

M13 bacteriophage production for large-scale applications.

Validation of a genomics-based hypothetical adverse outcome pathway: 2,4-dinitrotoluene perturbs PPAR signaling thus impairing energy metabolism and exercise endurance.

Coral-zooxanthellae meta-transcriptomics reveals integrated response to pollutant stress.

DNA binding and condensation properties of the herpes simplex virus type 1 triplex protein VP19C.

New derivatives of lupane triterpenoids disturb breast cancer mitochondria and induce cell death.

Top-level dynamics and the regulated gene response of feed-forward loop transcriptional motifs.

Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio).

Systematic Omics Analysis Review (SOAR) tool to support risk assessment.

MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity.

Systems toxicology identifies mechanistic impacts of 2-amino-4,6-dinitrotoluene (2A-DNT) exposure in Northern Bobwhite.

Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper.

Ecotoxicogenomics: Microarray interlaboratory comparability.

Adverse Outcome Pathways for Regulatory Applications: Examination of Four Case Studies With Different Degrees of Completeness and Scientific Confidence.

Ionotropic GABA receptor antagonism-induced adverse outcome pathways for potential neurotoxicity biomarkers.

Transcriptional Network Growing Models Using Motif-Based Preferential Attachment.

Relating suborganismal processes to ecotoxicological and population level endpoints using a bioenergetic model.

A weight of evidence assessment approach for adverse outcome pathways.

Predicting Fecundity of Fathead Minnows (Pimephales promelas) Exposed to Endocrine-Disrupting Chemicals Using a MATLAB®-Based Model of Oocyte Growth Dynamics.

Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles.

Tissue explant co-culture model of the hypothalamic-pituitary-gonadal-liver axis of the fathead minnow (Pimephales promelas) as a predictive tool for endocrine disruption.

Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds.

The Next Generation of Risk Assessment Multiyear Study- Highlights of Findings, Applications to Risk Assessment and Future Directions.

Daphnia magna's sense of competition: intra-specific interactions (ISI) alter life history strategies and increase metals toxicity.

Effects of the anti-microbial contaminant triclocarban, and co-exposure with the androgen 17β-trenbolone, on reproductive function and ovarian transcriptome of the fathead minnow (Pimephales promelas).

Novel enhanced applications of QSPR models: Temperature dependence of aqueous solubility.