@article{becker_moorman_deperno_simons_2013, title={Quantifiable Long-term Monitoring on Parks and Nature Preserves}, volume={12}, ISSN={["1938-5412"]}, DOI={10.1656/058.012.0208}, abstractNote={Abstract 
 Herpetofauna have declined globally, and monitoring is a useful approach to document local and long-term changes. However, monitoring efforts often fail to account for detectability or follow standardized protocols. We performed a case study at Hemlock Bluffs Nature Preserve in Cary, NC to model occupancy of focal species and demonstrate a replicable long-term protocol useful to parks and nature preserves. From March 2010 to 2011, we documented occupancy of Ambystoma opacum (Marbled Salamander), Plethodon cinereus (Red-backed Salamander), Carphophis amoenus (Eastern Worm Snake), and Diadophis punctatus (Ringneck Snake) at coverboard sites and estimated breeding female Ambystoma maculatum (Spotted Salamander) abundance via dependent double-observer egg-mass counts in ephemeral pools. Temperature influenced detection of both Marbled and Red-backed Salamanders. Based on egg-mass data, we estimated Spotted Salamander abundance to be between 21 and 44 breeding females. We detected 43 of 53 previously documented herpetofauna species. Our approach demonstrates a monitoring protocol that accounts for factors that influence species detection and is replicable by parks or nature preserves with limited resources.}, number={2}, journal={SOUTHEASTERN NATURALIST}, author={Becker, Sharon and Moorman, Christopher and DePerno, Christopher and Simons, Theodore}, year={2013}, month={Jun}, pages={339–352} }
 @article{becker_thomas_trifonov_wayne_graphodatsky_breen_2011, title={Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes}, volume={19}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-011-9233-4}, number={6}, journal={CHROMOSOME RESEARCH}, author={Becker, Shannon E. Duke and Thomas, Rachael and Trifonov, Vladimir A. and Wayne, Robert K. and Graphodatsky, Alexander S. and Breen, Matthew}, year={2011}, month={Aug}, pages={685–708} }
 @article{thomas_duke_wang_breen_higgins_linder_ellis_langford_dickinson_olby_et al._2009, title={‘Putting our heads together’: insights into genomic conservation between human and canine intracranial tumors}, volume={94}, ISSN={0167-594X 1573-7373}, url={http://dx.doi.org/10.1007/s11060-009-9877-5}, DOI={10.1007/s11060-009-9877-5}, abstractNote={Numerous attributes render the domestic dog a highly pertinent model for cancer-associated gene discovery. We performed microarray-based comparative genomic hybridization analysis of 60 spontaneous canine intracranial tumors to examine the degree to which dog and human patients exhibit aberrations of ancestrally related chromosome regions, consistent with a shared pathogenesis. Canine gliomas and meningiomas both demonstrated chromosome copy number aberrations (CNAs) that share evolutionarily conserved synteny with those previously reported in their human counterpart. Interestingly, however, genomic imbalances orthologous to some of the hallmark aberrations of human intracranial tumors, including chromosome 22/NF2 deletions in meningiomas and chromosome 1p/19q deletions in oligodendrogliomas, were not major events in the dog. Furthermore, and perhaps most significantly, we identified highly recurrent CNAs in canine intracranial tumors for which the human orthologue has been reported previously at low frequency but which have not, thus far, been associated intimately with the pathogenesis of the tumor. The presence of orthologous CNAs in canine and human intracranial cancers is strongly suggestive of their biological significance in tumor development and/or progression. Moreover, the limited genetic heterogenity within purebred dog populations, coupled with the contrasting organization of the dog and human karyotypes, offers tremendous opportunities for refining evolutionarily conserved regions of tumor-associated genomic imbalance that may harbor novel candidate genes involved in their pathogenesis. A comparative approach to the study of canine and human intracranial tumors may therefore provide new insights into their genetic etiology, towards development of more sophisticated molecular subclassification and tailored therapies in both species.}, number={3}, journal={Journal of Neuro-Oncology}, publisher={Springer Science and Business Media LLC}, author={Thomas, Rachael and Duke, Shannon E. and Wang, Huixia J. and Breen, Tessa E. and Higgins, Robert J. and Linder, Keith E. and Ellis, Peter and Langford, Cordelia F. and Dickinson, Peter J. and Olby, Natasha J. and et al.}, year={2009}, month={Mar}, pages={333–349} }
 @article{thomas_duke_karlsson_evans_ellis_lindblad-toh_langford_breen_2008, title={A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis}, volume={122}, ISSN={["1424-859X"]}, DOI={10.1159/000163088}, abstractNote={Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species. We have used the dog genome sequence assembly to identify a framework panel of 2,097 bacterial artificial chromosome (BAC) clones, selected at intervals of approximately one megabase. Each clone has been evaluated by multicolor fluorescence in situ hybridization (FISH) to confirm its unique cytogenetic location in concordance with its reported position in the genome assembly, providing new information on the organization of the dog genome. This panel of BAC clones also represents a powerful cytogenetic resource with numerous potential applications. We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy. We also show how individual clones selected from the BAC panel can be used as FISH probes in direct evaluation of tumor karyotypes, to verify and explore CNAs detected using aCGH analysis. This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.}, number={2}, journal={CYTOGENETIC AND GENOME RESEARCH}, author={Thomas, R. and Duke, S. E. and Karlsson, E. K. and Evans, A. and Ellis, P. and Lindblad-Toh, K. and Langford, C. F. and Breen, M.}, year={2008}, pages={110–121} }
 @article{thomas_duke_bloom_breen_young_feiste_seiser_tsai_langford_ellis_et al._2007, title={A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog}, volume={98}, ISSN={["0022-1503"]}, DOI={10.1093/jhered/esm053}, abstractNote={The generation of a 7.5x dog genome assembly provides exciting new opportunities to interpret tumor-associated chromosome aberrations at the biological level. We present a genomic microarray for array comparative genomic hybridization (aCGH) analysis in the dog, comprising 275 bacterial artificial chromosome (BAC) clones spaced at intervals of approximately 10 Mb. Each clone has been positioned accurately within the genome assembly and assigned to a unique chromosome location by fluorescence in situ hybridization (FISH) analysis, both individually and as chromosome-specific BAC pools. The microarray also contains clones representing the dog orthologues of 31 genes implicated in human cancers. FISH analysis of the 10-Mb BAC clone set indicated excellent coverage of each dog chromosome by the genome assembly. The order of clones was consistent with the assembly, but the cytogenetic intervals between clones were variable. We demonstrate the application of the BAC array for aCGH analysis to identify both whole and partial chromosome imbalances using a canine histiocytic sarcoma case. Using BAC clones selected from the array as probes, multicolor FISH analysis was used to further characterize these imbalances, revealing numerous structural chromosome rearrangements. We outline the value of a combined aCGH/FISH approach, together with a well-annotated dog genome assembly, in canine and comparative cancer studies.}, number={5}, journal={JOURNAL OF HEREDITY}, author={Thomas, Rachael and Duke, Shannon E. and Bloom, Stephanie K. and Breen, Tessa E. and Young, Andrea C. and Feiste, Erika and Seiser, Eric L. and Tsai, Pei-Chien and Langford, Cordelia F. and Ellis, Peter and et al.}, year={2007}, pages={474–484} }
 @article{kisseberth_nadella_breen_thomas_duke_murahari_kosarek_vernau_avery_burkhard_et al._2007, title={A novel canine lymphoma cell line: A translational and comparative model for lymphoma research}, volume={31}, ISSN={["1873-5835"]}, DOI={10.1016/j.leukres.2007.04.003}, abstractNote={A novel canine lymphoma cell line, OSW, was established from the malignant pleural effusion of a dog with peripheral T-cell lymphoma. The immunoprofile as determined by flow cytometry was as follows: positive for CD45, CD49d, CD18, CD11a; weakly positive for CD11b, CD11c, CD11d; and negative for CD45RA, CD1a, CD1c, CD3, TCRαβ, TCRγδ, CD4, CD5, CD8a, CD8b, CD90(Thy1), CD21, MHCII, CD14(TUK4), CD34, and MPO. Immunocytochemistry of cytospin preparations was negative for cytoplasmic CD3, CD79a, and MPO, but was positive for CD20. The cell line had an oligoclonal T-cell receptor gamma (TCRγ) gene rearrangement. Array comparative genomic hybridization (aCGH) and single locus probe (SLP) analysis showed that there were copy number increases of loci on dog chromosome 13 (CFA 13), and copy number decreases were evident for regions of CFA 11, 22, 26, 30 and 32, which include several of the more common chromosomal aberrations reported previously in canine lymphoma. The OSW cell line grows rapidly in vitro and is tumorigenic as a xenograft in SCID/NOD mice. OSW represents one of only a few reported canine lymphoma cell lines and is the most thoroughly characterized. This cell line and xenograft represent significant in vitro and in vivo models, respectively, for comparative and translational lymphoma research.}, number={12}, journal={LEUKEMIA RESEARCH}, author={Kisseberth, William C. and Nadella, Murali Vara Prasad and Breen, Matthew and Thomas, Rachael and Duke, Shannon E. and Murahari, Sridhar and Kosarek, Carrie E. and Vernau, William and Avery, Anne C. and Burkhard, Mary Jo and et al.}, year={2007}, month={Dec}, pages={1709–1720} }
 @misc{mikkelsen_wakefield_aken_amemiya_chang_duke_garber_gentles_goodstadt_heger_et al._2007, title={Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences}, volume={447}, ISSN={["1476-4687"]}, DOI={10.1038/nature05805}, abstractNote={We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.}, number={7141}, journal={NATURE}, author={Mikkelsen, Tarjei S. and Wakefield, Matthew J. and Aken, Bronwen and Amemiya, Chris T. and Chang, Jean L. and Duke, Shannon and Garber, Manuel and Gentles, Andrew J. and Goodstadt, Leo and Heger, Andreas and et al.}, year={2007}, month={May}, pages={167–U1} }
 @article{davidow_breen_duke_samollow_mccarrey_lee_2007, title={The search for a marsupial XIC reveals a break with vertebrate synteny}, volume={15}, ISSN={1573-6849}, url={http://dx.doi.org/10.1007/s10577-007-1121-6}, DOI={10.1007/s10577-007-1121-6}, number={2}, journal={Chromosome Research}, publisher={Springer Science and Business Media LLC}, author={Davidow, Lance S. and Breen, Matthew and Duke, Shannon E. and Samollow, Paul B. and McCarrey, John R. and Lee, Jeannie T.}, year={2007}, month={Feb}, pages={137–146} }
 @article{duke_samallow_mauceli_lindblad-toh_breen, title={Cytogenetic BAC map of the genome of Monodelphis domestica}, volume={15}, journal={Chromosome Research}, author={Duke, S. E. and Samallow, P. and Mauceli, E. and Lindblad-Toh, K. and Breen, M.}, pages={3610–3670} }