Julie C. Dunning Hotopp

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Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis

C. Fraser, M. Chibucos, L. Tallon, 2014, BMC Genomics.

Endosymbiont DNA in Endobacteria-Free Filarial Nematodes Indicates Ancient Horizontal Genetic Transfer

Samantha N. McNulty, B. Slatko, M. Mitreva, 2010, PloS one.

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

David R. Riley, Samuel V. Angiuoli, H. Tettelin, 2010, Genome Biology.

Multilocus Sequence Typing System for the Endosymbiont Wolbachia pipientis

H. Tettelin, J. Werren, M. Maiden, 2006, Applied and Environmental Microbiology.

Horizontal gene transfer between bacteria and animals.

Julie C. Dunning Hotopp, Julie C. Dunning Hotopp, 2011, Trends in genetics : TIG.

X-ray crystal structure of Escherichia coli taurine/alpha-ketoglutarate dioxygenase complexed to ferrous iron and substrates.

J. Elkins, M. J. Ryle, R. Hausinger, 2002, Biochemistry.

Comparative Genomics of Emerging Human Ehrlichiosis Agents

Jonathan Crabtree, Jaideep P. Sundaram, Rekha Seshadri, 2006, PLoS genetics.

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Jonathan Crabtree, Kelly M. Robinson, J. Mattick, 2017, Microbiome.

The two-component response regulator LiaR regulates cell wall stress responses, pili expression and virulence in group B Streptococcus.

H. Tettelin, N. Ishmael, L. Madoff, 2013, Microbiology.

Comparison of long read sequencing technologies in resolving bacteria and fly genomes

D. Rasko, L. Tallon, Xuechu Zhao, 2020, bioRxiv.

Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis

Xin Wang, Lee H. Harrison, Mary G. Krauland, 2015, EBioMedicine.

Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.

H. Tettelin, R. Rappuoli, D. Fouts, 2006, Microbiology.

Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi

David R. Riley, J. Foster, J. White, 2013, BMC Genomics.

Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences

T. Conrads, T. O’Connor, M. D. Kessler, 2019, Cancer.

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

James B. Munro, Zalak V. Shah, Joana C. Silva, 2020, Genome medicine.

Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements

D. Rasko, J. Matthijnssens, J. Stajich, 2020, Microbiology Resource Announcements.

Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells

David R. Riley, U. Farooq, T. Creasy, 2013, BMC Genomics.

Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection

David R. Riley, H. Tettelin, J. Scott, 2013, BMC Genomics.

Draft genome sequence of the Wolbachia endosymbiont of Wuchereria bancrofti wWb

D. Serre, Julie C. Dunning Hotopp, P. Zimmerman, 2017, Pathogens and disease.

Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement

J. Mattick, L. Tallon, Xuechu Zhao, 2022, Current Biology.

Complete Genome Sequence of wBp, the Wolbachia Endosymbiont of Brugia pahangi FR3

J. Mattick, J. Foster, Suvarna Nadendla, 2020, Microbiology Resource Announcements.

The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont

Julie C. Dunning Hotopp, L. Klasson, 2018, G3: Genes, Genomes, Genetics.

Lateral gene transfer between prokaryotes and eukaryotes.

Karsten B. Sieber, Julie C. Dunning Hotopp, Robin E. Bromley, 2017, Experimental cell research.

Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer

T. Creasy, L. Tallon, N. Kumar, 2012, BMC Research Notes.

Biology wars: the eukaryotes strike back.

Julie C. Dunning Hotopp, A. Estes, 2014, Cell host & microbe.

Comparative genomics of the Erwinia and Enterobacter olive fly endosymbionts

David J Hearn, Sonia Agrawal, Julie C. Dunning Hotopp, 2018, Scientific Reports.

Draft Genome Sequence of Enterobacter sp. Strain OLF, a Colonizer of Olive Flies

David J Hearn, Suvarna Nadendla, Julie C. Dunning Hotopp, 2018, Microbiology Resource Announcements.

Draft Genome Sequence of Erwinia dacicola, a Dominant Endosymbiont of Olive Flies

David J Hearn, Suvarna Nadendla, Julie C. Dunning Hotopp, 2018, Microbiology Resource Announcements.

Nearly Complete Genome Sequence of Brugia malayi Strain FR3

Tyson A. Clark, J. Korlach, N. Holroyd, 2020, Microbiology Resource Announcements.

Brood Ball-Mediated Transmission of Microbiome Members in the Dung Beetle, Onthophagus taurus (Coleoptera: Scarabaeidae)

E. Snell-Rood, David J Hearn, A. Moczek, 2013, PloS one.

Multispecies Transcriptomics Data Set of Brugia malayi, Its Wolbachia Endosymbiont wBm, and Aedes aegypti across the B. malayi Life Cycle

J. Foster, L. Tallon, N. Kumar, 2018, Microbiology Resource Announcements.

Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production

H. Tettelin, N. Kumar, Julie C. Dunning Hotopp, 2011, PloS one.

Intrinsic tryptophan fluorescence as a probe of metal and alpha-ketoglutarate binding to TfdA, a mononuclear non-heme iron dioxygenase.

R. Hausinger, D. Hogan, Julie C. Dunning Hotopp, 2003, Journal of inorganic biochemistry.

Probing the 2,4-dichlorophenoxyacetate/alpha-ketoglutarate dioxygenase substrate-binding site by site-directed mutagenesis and mechanism-based inactivation.

R. Hausinger, Julie C. Dunning Hotopp, 2002, Biochemistry.

Evaluation of a high-throughput, cost-effective Illumina library preparation kit

Joana C. Silva, D. Rasko, L. Tallon, 2021, Scientific Reports.

Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease

C. Fraser, S. Daugherty, Naomi A. Sengamalay, 2017, Microbial biotechnology.

Using Core Genome Alignments To Assign Bacterial Species

James B. Munro, H. Tettelin, Julie C. Dunning Hotopp, 2018, mSystems.

X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes

J. Mattick, J. Foster, R. Rao, 2021, PLoS neglected tropical diseases.

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

James B. Munro, Zalak V. Shah, Joana C. Silva, 2019, Genome Medicine.

Best practices on the differential expression analysis of multi-species RNA-seq

Christina A. Cuomo, D. Rasko, J. Livny, 2021, Genome Biology.

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

C. Fraser, J. Foster, D. Rasko, 2018, Scientific Reports.

A Review of Bacteria-Animal Lateral Gene Transfer May Inform Our Understanding of Diseases like Cancer

Karsten B. Sieber, Julie C. Dunning Hotopp, K. Robinson, 2013, PLoS genetics.

Grafting or pruning in the animal tree: lateral gene transfer and gene loss?

J. Hotopp, Julie C. Dunning Hotopp, 2018, BMC Genomics.

Grafting or pruning in the animal tree: lateral gene transfer and gene loss?

Julie C. Dunning Hotopp, 2017, BMC Genomics.

Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen.

Julie C. Dunning Hotopp, Kelly M. Robinson, Julie C. Dunning Hotopp, 2014, Cancer letters.

Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae

Karsten B. Sieber, S. Andersson, L. Tallon, 2014, BMC Genomics.

Extensive genomic diversity of closely related Wolbachia strains.

H. Tettelin, J. Werren, V. Nene, 2009, Microbiology.

Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species

Mihai Pop, Steven L Salzberg, Julie C Dunning Hotopp, 2005, Genome Biology.

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data

Ricky S. Adkins, Joana C. Silva, C. Fraser, 2017, Microbial genomics.

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

Julie C Dunning Hotopp, David R. Riley, Rino Rappuoli, 2011, Proceedings of the National Academy of Sciences.

Sex chromosome evolution in parasitic nematodes of humans

Tyson A. Clark, J. Korlach, N. Holroyd, 2020, Nature Communications.

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics

J. Foster, L. Tallon, N. Kumar, 2019, mSystems.

Complete Mitochondrial Genome Sequence of Mansonella perstans

A. Hoerauf, Suvarna Nadendla, L. Tallon, 2020, Microbiology Resource Announcements.

Modeling the integration of bacterial rRNA fragments into the human cancer genome

Karsten B. Sieber, Julie C. Dunning Hotopp, Pawel Gajer, 2016, BMC Bioinformatics.

Comparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis

C. Fraser, S. Daugherty, Naomi A. Sengamalay, 2021, BMC genomics.

In Vivo-Selected Compensatory Mutations Restore the Fitness Cost of Mosaic penA Alleles That Confer Ceftriaxone Resistance in Neisseria gonorrhoeae

M. Unemo, Julie C. Dunning Hotopp, R. Nicholas, 2018, mBio.

Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

D. Rasko, C. E. Hjelmen, J. Johnston, 2021, G3.

Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity

David A Baltrus, Christina A Cuomo, John J Dennehy, 2019, Microbiology Resource Announcements.

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis

C. Fraser, M. Chibucos, L. Tallon, 2014, BMC Genomics.

Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae

Suvarna Nadendla, Julie C. Dunning Hotopp, M. Gasser, 2019, Microbiology Resource Announcements.

Sex chromosome evolution in parasitic nematodes of humans

Tyson A. Clark, J. Korlach, N. Holroyd, 2020, Nature Communications.

Whole-Genome Association Study on Tissue Tropism Phenotypes in Group A Streptococcus

David R. Riley, Scott V. Nguyen, H. Tettelin, 2011, Journal of bacteriology.

TwinBLAST: When Two Is Better than One

Jonathan Crabtree, Julie C Dunning Hotopp, Anup Mahurkar, 2019, Microbiology Resource Announcements.

FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses

Ricky S. Adkins, C. Fraser, J. Mattick, 2021, mSystems.

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

C. Fraser, J. Foster, D. Rasko, 2018, bioRxiv.

Isolation of a divergent strain of Rickettsia japonica from Dew's Australian bat Argasid ticks (Argas (Carios) dewae) in Victoria, Australia.

Julie C. Dunning Hotopp, L. Izzard, J. Stenos, 2018, Ticks and tick-borne diseases.

Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and cannot say.

H. Tettelin, J. Werren, K. Bourtzis, 2008, Molecular biology and evolution.

Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples

C. Fraser, S. Daugherty, L. Tallon, 2016, Scientific Reports.

Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells

Hong Liu, Julie C. Dunning Hotopp, S. Filler, 2018, Microbial genomics.

Nearly Complete Genome Sequence of Brugia pahangi FR3

J. Mattick, J. Foster, Suvarna Nadendla, 2020, Microbiology Resource Announcements.

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics

C. Fraser, J. Mattick, D. Rasko, 2019, Microbial genomics.

Cost Effective, Experimentally Robust Differential Expression Analysis for Human/Mammalian, Pathogen, and Dual-Species Transcriptomics

C. Fraser, D. Rasko, A. Shetty, 2018, bioRxiv.

FADU: A Feature Counting Tool for Prokaryotic RNA-Seq Analysis

Ricky S. Adkins, C. Fraser, D. Rasko, 2018, bioRxiv.

Extensive genomic diversity of closely related Wolbachia strains.

H. Tettelin, J. Werren, V. Nene, 2009, Microbiology.

Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.

H. Tettelin, R. Rappuoli, D. Fouts, 2006, Microbiology.

Genomics of Loa Loa, a Wolbachia-free Filarial Parasite of Humans Genomics of Loa Loa, a Wolbachia-free Filarial Parasite of Humans Nih Public Access Author Manuscript

C. Russ, J. Wortman, J. Hotopp, 2022 .

Improved metagenome assemblies through selective enrichment of bacterial genomic DNA from eukaryotic host genomic DNA using ATAC-seq

Julie C. Dunning Hotopp, Lindsey J. Cantin, Jeremy M. Foster, 2024, Frontiers in microbiology.

Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs

Julie C. Dunning Hotopp, Amelia R. I. Lindsey, M. Gasser, 2023, Life Science Alliance.