Biology Faculty Articles

Biology Faculty Articles

 

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Submissions from 2018

Forensic DNA Analysis, Bruce R. McCord, Quentin Gauthier, Sohee Cho, Meghan N. Roig, Georgiana C. Gibson-Daw, Brian Young, Fabiana Taglia, Sara C. Zapico, Roberta Fogliatto Mariot, Steven B. Lee, and George Duncan

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Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments, Maria A. Nieves-Colon, Andrew T. Ozga, William J. Pestle, Andrea Cucina, Vera Tiesler, Travis W. Stanton, and Anne C. Stone

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Foreword, Stephen J. O'Brien

Deep Mitochondrial Lineage Divergence Among Populations of the Southern Stingray (Hypanus americanus (Hildebrand & Schroeder, 1928)) Throughout the Southeastern United States and Caribbean, Vincent P. Richards, Melissa B. DeBiasse, and Mahmood S. Shivji

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The Successful Exploitation of Urban Environments by the Golden Silk Spider, Nephila clavipes (Araneae, Nephilidae), Jake Ripp, Omar T. Eldakar, Andrew C. Gallup, and Paul T. Arena

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Treatment Outcomes of Mohs Surgery vs. Imiquimod in Basal Cell Carcinoma, Mir Saleem and Julianna Robinson

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Deep-Sea Hydrothermal Vents as Natural Egg-Case Incubators at the Galapagos Rift, Pelayo Salinas-de-Leon, Brennan Phillips, David A. Ebert, Mahmood S. Shivji, Florencia Cerutti-Pereyra, Cassandra Ruck, Charles R. Fisher, and Leigh Marsh

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The Importance of Preventative Medicine in Conjunction with Modern Day Genetic Studies, Sierra Sandler, Lauren Alfino, and Mir Saleem

Convergence of marine megafauna movement patterns in coastal and open oceans, A. M.M. Sequeira, J. P. Rodriguez, Victor M. Eguiluz, R. Harcourt, M. Hindell, D. W. Sims, C. M. Duarte, D. P. Costa, J. Fernández-Gracia, L. C. Ferreira, G. C. Hays, M. R. Heupel, M. G. Meekan, A. Aven, F. Bailleul, A. M.M. Baylis, M. L. Berumen, C. D. Braun, J. Burns, M. J. Caley, R. Campbell, R. H. Carmichael, Erik G. Clua, L. D. Einoder, Ari Friedlaender, M E. Goebel, S. D. Goldsworthy, C. Guinet, J. Gunn, D. Hamer, N. Hammerschlag, M. Hammill, L. A. Hückstädt, N. E. Humphries, M. -A. Lea, A. Lowther, A. Mackay, E. McHuron, J. McKenzie, L. McLeay, C. R. McMahon, K. Mengersen, M. M. C. Muelbert, A. M. Pagano, B. Page, N. Queiroz, P. W. Robinson, S. A. Shaffer, Mahmood Shivji, G. B. Skomal, S. R. Thorrold, S. Villegas-Amtmann, M. Weise, R. Wells, Bradley M. Wetherbee, A. Wiebkin, B. Wienecke, and M. Thums

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Characterisation and monitoring of one of the world's most valuable ecotourism animals, the southern stingray at Stingray City, Grand Cayman, Jeremy J. Vaudo, Bradley M. Wetherbee, Guy C.M. Harvey, Jessica C. Harvey, Alexandra J.F. Prebble, Mark J. Corcoran, Matthew D. Potenski, Keith A. Bruni, Robert T. Leaf, Alan D. Henningsen, Jeremy S. Collie, and Mahmood S. Shivji

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Identified OAS3 gene variants associated with coexistence of HBsAg and anti-HBs in chronic HBV infection, S. Wang, J. Wang, M. J. Fan, T. Y. Li, H. Pan, X. Wang, H. K. Liu, Q. F. Lin, J. G. Zhang, L. P. Guan, D. V. Zhernakova, S. J. O’Brien, Z. R. Feng, L. Chang, E. H. Dai, J. H. Lu, H. L. Xi, Z. Zeng, Y. Y. Yu, and B. B. Wang

Culture-Independent Characterization of the Microbiome of Healthy Pulp, Christopher Widmer, Jorie L. Skutas, Cole Easson, Jose Lopez, Calvin Torneck, Michael Flax, and Taner Cem Sayin

Marker of proliferation Ki-67 expression is associated with transforming growth factor beta 1 and can predict the prognosis of patients with hepatic B virus-related hepatocellular carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, and Tao Peng

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Analytical “Bake-Off” of Whole Genome Sequencing Quality for the Genome Russia Project Using a Small Cohort for Autoimmune Hepatitis, Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David L. Valle, Minzhong Tang, Emilia Shin, Kathleen B. Schwarz, and Stephen James O'Brien

Submissions from 2017

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The Sunflower Genome Provides Insights into Oil Metabolism, Flowering and Asterid Evolution, Hélène Badouin, Jérôme Gouzy, Christopher Grassa, Florent Murat, S. Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill, Nolan Kane, John Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile Donnadieu, Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven Knapp, Zhao Lai, Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer Mandel, Gwenola Marage, Gwenaëlle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savithri Nambeesan, Thuy Nguyen, Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas, Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John Burke, Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren Rieseberg, and Nicolas Langlade

Mitogenomic Sequences Support a North–South Subspecies Subdivision within Solenodon paradoxus, Adam L. Brandt, Kirill Grigorev, Yashira M. Afanador-Hernandez, Liz A. Paulino, William J. Murphy, Adrell Nunez, Aleksey Komissarov, Jessica R. Brandt, Pavel Dobrynin, J. David Hernandez-Martich, Roberta Maria, Stephen J. O'Brien, Luis Rodriguez, Juan C. Martinez-Cruzado, T. K. Oleksyk, and Alfred L. Roca

Host Abundance, Seagrass Cover, and Temperature Predict Infection Rates of Parasitic Isopods (Bopyridae) on Caridean Shrimp., Sarah A. Briggs, Christopher Blanar, Michael B. Robblee, Christopher B. Boyko, and Amy Hirons

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FlipTube™ technology promotes clean manipulation of forensic samples on automated robotic workstations, Chris Comar, George Duncan, and Kevin W. P. Miller

Effects of the Pleistocene on the Mitochondrial Population Genetic Structure and Demographic History of the Silky Shark (Carcharhinus falciformis) in the Western Atlantic Ocean, Rodrigo R. Domingues, Alexandre W. S. Hilsdorf, Mahmood S. Shivji, Fabio H.V. Hazin, and O. B. F. Gadig

Synthetically Engineered Microbes Reveal Interesting Principles of Cooperation, Michael D. Dressler, Corey J. Clark, Chelsea A. Thachettu, Yasmine Zakaria, Omar Tonsi Eldakar, and Robert P. Smith

Acute Physical Stress Modulates the Temporal Expression of Self-Reported Contagious Yawning in Humans, Omar Tonsi Eldakar, Jaime Tartar, Daniel Garcia, Valentina Ramirez, Melissa Dauzonne, Yana Armani, and Andrew C. Gallup

Untangling the Cecal Microbiota of Feral Chickens by Culturomic and Metagenomic Analyses, Chiara Ferrario, Giulia Alessandri, Leonardo Mancabelli, Eben Gering, Marta Mangifesta, Christian Milani, Gabriele Andrea Lugli, Alice Viappiani, Sabrina Duranti, Francesca Turroni, Maria Cristina Ossiprandi, Ricardo Hiyashi, Roderick Mackie, Douwe van Sinderen, and Marco Ventura

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Genome-wide signatures of complex introgression and adaptive evolution in the big cats, Henrique V. Figueiró, Gang Li, Fernanda J. Trindade, Juliana Assis, Fabiano Pais, Gabriel Fernandes, Sarah H.D. Santos, Graham M. Hughes, Aleksey Komissarov, Agostinho Antunes, Cristine S. Trinca, Maíra R. Rodrigues, Tyler Linderoth, Ke Bi, Leandro Silveira, Fernando C.C. Azevedo, Daniel Kantek, Emiliano Ramalho, Ricardo A. Brassaloti, Priscilla M.S. Villela, Adauto L.V. Nunes, Rodrigo H.F. Teixeira, Ronaldo G. Morato, Damian Loska, Patricia Saragüeta, Toni Gabaldón, Emma C. Teeling, Stephen J. O'Brien, and Rasmus Nielsen

The Complete Mitochondrial Genome of the Critically Endangered Angelshark, Squatina squatina, Cristin Keelin Fitzpatrick, Kimberly A. Finnegan, Filip Osaer, Krupskaya Narvaez, and Mahmood S. Shivji

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Yawns Are Cool, Andrew C. Gallup and Omar T. Eldakar

Winner and Loser Effects in Collegiate Baseball and Softball Doubleheaders, Andrew C. Gallup, Omar T. Eldakar, Michael Schonning, and Michael Yanchus

Male‐Mimicking Females Increase Male‐Male Interactions, and Decrease Male Survival and Condition in a Female‐Polymorphic Damselfly, Eben Gering

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Complete mitogenome sequences of smooth hammerhead sharks, Sphyrna zygaena, from the eastern and western Atlantic, Derek S. Guy, Cassandra L. Ruck, Jose V. Lopez, and Mahmood S. Shivji

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The Human Microbiome: An Emerging Tool in Forensics, Jarrad T. Hampton-Marcell, Jose V. Lopez, and Jack A. Gilbert

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Perspectives Provided by Leopard and Other Cat Genomes: How Diet Determined the Evolutionary History of Carnivores, Omnivores, and Herbivores, Soonok Kim, Yun Sung Cho, Jong Bhak, Stephen J. O'Brien, and Joo-Hong Yeo

Larger Females are Choosier in the Gray Treefrog (Hyla versicolor), Michael C. Kuczynski, Thomas Getty, and Eben Gering

Signal Localization: A New Approach in Signal Discovery, Sergey Malov, Alexey Antonik, Minzhong Tang, Alexandre Berred, Yi Zeng, and Stephen J. O'Brien

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Comparative Transcriptomics of Elasmobranchs and Teleosts Highlight Important Processes in Adaptive Immunity and Regional Endothermy, Nicholas J. Marra, Vincent P. Richards, Angela Early, Steve M. Bogdanowicz, Paulina D. Pavinski Bitar, Michael J. Stanhope, and Mahmood S. Shivji

Conservation Genetics of the Cheetah: Lessons Learned and New Opportunities, Stephen J. O'Brien, Warren E. Johnson, Carlos A. Driscoll, Pavel Dobrynin, and Laurie Marker

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Major Complications and Management Options of Obesity, Shreja Patel and Mir Saleem

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X Chromosome Evolution in Cetartiodactyla, Anastasiya A. Proskuryakova, Anastasia I. Kulemzina, Polina L. Perelman, Alexey I. Makunin, Denis M. Larkin, Marta Farre, Anna V. Kukekova, Jennifer Lynn Johnson, Natalya A. Lemskaya, Violetta R. Beklemisheva, M. Roelke-Parker, June Bellizzi, Oliver A. Ryder, Stephen James O'Brien, and Alexander S. Graphodatsky

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First record of the megamouth shark, Megachasma pelagios, (family Megachasmidae) in the tropical western North Atlantic Ocean, Grisel Rodriguez-Ferrer, Bradley M. Wetherbee, Michelle Schärer, Craig Lilyestrom, Jan P. Zegarra, and Mahmood Shivji

The Complete Mitochondrial Genome of the Endangered Great Hammerhead Shark, Sphyrna mokarran, Cassandra L. Ruck, Nicholas J. Marra, Mahmood S. Shivji, and Michael Stanhope

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Meditation Experience Associated with Structural Neuroplasticity, Mir Saleem and Pallavi Samudrala

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Complete mitochondrial genomes of Baikal oilfishes (Perciformes: Cottoidei), earth’s deepest-swimming freshwater fishes, Michael W. Sandel, Andres Aguilar, Kayla Fast, Stephen O’Brien, Alla Lapidus, David B. Allison, Veronika Teterina, and Sergei Kirilchik

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Evolution of Group I Introns in Porifera: New Evidence for Intron Mobility and Implications for DNA Barcoding, Astrid Schuster, Jose V. Lopez, Leontine E. Becking, Michelle Kelly, Shirley A. Pomponi, Gert Wörheide, Dirk Erpenbeck, and Paco Cárdenas

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Preoperative transcatheter arterial chemotherapy may suppress oxidative stress in hepatocellular carcinoma cells and reduce the risk of short-term relapse, Hao Su, Guangzhi Zhu, Ketut Indra Djaja P, Yi Lin, Yizhen Gong, Xiaoguang Liu, Jiaquan Li, Zhiming Liu, Xiao Qin, Lequn Li, Tangwei Liu, Zili Lu, Minyi Wei, Lunan Yan, Cheryl Ann Winkler, Stephen J. O'Brien, Jing Li, Kaiyin Xiao, and Tao Peng

Advancing Genomics Through the Global Invertebrate Genomics Alliance (GIGA), Christian R. Voolstra, GIGA Community of Scientists, Gert Wörheide, and Jose V. Lopez

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Cooperation and Competition Shape Ecological Resistance During Periodic Spatial Disturbance of Engineered Bacteria, Cortney E. Wilson, Allison J. Lopatkin, Travis J. A. Craddock, William W. Driscoll, Omar T. Eldakar, Jose V. Lopez, and Robert P. Smith

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Genome-Wide Analyses Reveal Gene Influence on HIV Disease Progression and HIV-1C Acquisition in Southern Africa, Wen Xie, Denis Agniel, Andrey Shevchenko, Sergey V. Malov, Anton Svitin, Nikolay Cherkasov, Marianna K. Baum, Adriana Campa, Simani Gaseitsiwe, Hermann Bussmann, Joseph Makhema, Richard Marlink, Vladimir Novitsky, Tun Hou Lee, Tianxi Cai, Stephen J. O'Brien, and M. Essex

Aldehyde dehydrogenase 1 (ALDH1) isoform expression and potential clinical implications in hepatocellular carcinoma, Cheng Kun Yang, Xiang Kun Wang, Xi Wen Liao, Chuang Ye Han, Ting Dong Yu, Wei Qin, Guang Zhi Zhu, Hao Su, Long Yu, Xiao Guang Liu, Si Cong Lu, Zhi Wei Chen, Zhen Liu, Ke Tuan Huang, Zheng Tao Liu, Yu Liang, Jian Lu Huang, Kai Yin Xiao, Min Hao Peng, Cheryl Ann Winkle, Stephen J. O’Brien, and Tao Peng

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Genome-Wide Association Study of MKI67 Expression and its Clinical Implications in HBV-Related Hepatocellular Carcinoma in Southern China, Cheng Kun Yang, Ting Dong Yu, Chuang Ye Han, Wei Qin, Xi Wen Liao, Long Yu, Xiao Guang Liu, Guang Zhi Zhu, Hao Su, Si Cong Lu, Zhi Wei Chen, Zhen Liu, Ke Tuan Huang, Zheng Tao Liu, Yu Liang, Jian Lu Huang, Zeng Nan Mo, Xue Qin, Lequn Li, Kai Yin Xiao, Min Hao Peng, Cheryl Ann Winkle, Stephen J. O'Brien, and Tao Peng

Submissions from 2016

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Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds, Daniela Almeida, Emanuel Maldonado, Imran Khan, Liliana Silva, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Warren E. Johnson, and Agostinho Antunes

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Forensic discrimination of vaginal epithelia by DNA methylation analysis through pyrosequencing, Joana Antunes, Deborah S. B. S. Silva, Kuppareddi Balamurugan, George Duncan, Clarice S. Alho, and Bruce McCord

High-resolution melt analysis of DNA methylation to discriminate semen in biological stains, Joana Antunes, Deborah S. B. S. Silva, Kuppareddi Balamurugan, George Duncan, Clarice S. Alho, and Bruce McCord

The genome-wide analysis of carcinoembryonic antigen signaling by colorectal cancer cells using RNA sequencing, Olga Bajenova, Anna Gorbunova, Igor Evsyukov, Michael Rayko, Svetlana Gapon, Ekaterina Bozhokina, Alexander Shishkin, and Stephen J. O'Brien

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The Asian Arowana (Scleropages formosus) Genome Provides New Insights into the Evolution of an Early Lineage of Teleosts, Chao Bian, Yinchang Hu, Vydianathan Ravi, Inna S. Kuznetsova, Xueyan Shen, Xidong Mu, Ying Sun, Xinxin You, Jia Li, Xiaofeng Li, Ying Qiu, Boon-Hui Tay, Natascha May Thevasagayam, Aleksey S. Komissarov, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Jianren Luo, Yi Liu, Hongmei Song, Chao Liu, Xuejie Wang, Dangen Gu, Yexin Yang, Wujiao Li, Gianluca Polgar, Guangyi Fan, Peng Zeng, He Zhang, Zijun Xiong, Zhujing Tang, Chao Peng, Zhiqiang Ruan, Hui Yu, Jieming Chen, Mingjun Fan, Yu Huang, Min Wang, Xiaomeng Zhao, Guojun Hu, Huanming Yang, Jian Wang, Jun Wang, Xun Xu, Linsheng Song, Gangchun Xu, Junmin Xu, Stephen J. O'Brien, Laszlo Orban, Byrappa Venkatesh, and Qiong Shi

Parasite Community Similarity in Athabasca River Trout-Perch (Percopsis omiscomaycus) Varies with Local-Scale Land Use and Sediment Hydrocarbons, but Not Distance or Linear Gradients, Christopher Blanar, M. Hewitt, M. McMaster, J. Kirk, Z. Wang, W. Norwood, and D. J. Marcogliese

Pangolin genomes and the evolution of mammalian scales and immunity, Siew Who Choo, Mike Rayko, Tze King Tan, Ranjeev Hari, Aleksey Komissarov, Wei Yee Wee, Andrey A. Yurchenko, Sergey Kliver, Gaik Tamazian, Agostinho Antunes, Richard K. Wilson, Wesley C. Warren, Klaus Peter Koepfli, Patrick Minx, Ksenia Krasheninnikova, Antoinette Kotze, Desire L. Dalton, Elaine Vermaak, Ian C. Paterson, Pavel Dobrynin, Frankie Thomas Sitam, Jeffrine J. Rovie-Ryan, Warren E. Johnson, Aini Mohamed Yusoff, Shu Jin Luo, Kayal Vizi Karuppannan, Gang Fang, Deyou Zheng, and Mark B. Gerstein

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The Interplay of TLR9, Myeloid Cells, and A20 in Periodontal Inflammation, Katie E. Crump, Jennifer C. Oakley, Xia Xia-Juan, Theandra C. Madu, Swathi Devaki, Erin C. Mooney, and Sinem E. Sahingur

Microbial Nucleic Acid Sensing in Oral and Systemic Diseases, Katie E. Crump and S. E. Sahingur

Shared Phylogeographical Breaks in a Caribbean Coral Reef Sponge and Its Invertebrate Commensals, M. B. DeBiasse, Vincent P. Richards, Mahmood S. Shivji, and Michael E. Hellberg

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Adaptive Myopia: How Nearsightedness on Land Helps Us Underwater, Omar T. Eldakar and Andrew C. Gallup

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application, Brittany A. Garner, Brian K. Hand, Stephen J. Amish, Louis Bernatchez, Jeffrey T. Foster, Kristina M. Miller, Phillip A. Morin, Shawn R. Narum, Stephen J. O'Brien, William D. Templin, Paul Sunnucks, Jeffrey Strait, Kenneth I. Warheit, Todd R. Seamons, John Wenburg, Jeffrey Olsen, and Gordon Luikart

Ecology and Evolution of Phenotypic Plasticity in the Penis and Cirri of Barnacles, J. Matthew Hoch, Daniel T. Schneck, and Christopher J. Neufeld

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Highly Distinct Chromosomal Structures in Cowpea (Vigna unguiculata), as Revealed by Molecular Cytogenetic Analysis, Aiko Iwata-Otsubo, Jer-Young Lin, Navdeep Gill, and Scott Jackson

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Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc, Choongwon Jeong, Andrew T. Ozga, David B. Witonsky, Helena Malmstrom, Hanna Edlund, Courtney A. Hofman, Richard W. Hagan, Mattias Jakobsson, Cecil M. Lewis Jr., Mark Aldenderfer, Anna Di Rienzo, and Christina Warinner

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Feralisation Targets Different Genomic Loci to Domestication in the Chicken, M. Johnsson, Eben Gering, P. Willis, S. Lopez, L. Van Dorp, G. Hellenthal, R. Henriksen, U. Friberg, and D. Wright

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly, Soonok Kim, Yun Sung Cho, Hak Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim, Je Hoon Jun, Hye Jin Lee, Suan Cho, Olga Uphyrkina, Aleksey Kostyria, John Goodrich, Dale Miquelle, Melody Roelke, John Lewis, Andrey Yurchenko, Anton Bankevich, Juok Cho, and Semin Lee

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The complete mitochondrial genome of the parthenogenetic Caucasian rock lizard Darevskia unisexualis (Squamata: Lacertidae) contains long tandem repeat formed by 59 bp monomer, Aleksey Komissarov, Vitaly Korchagin, Sergei Kliver, Pavel Dobrynin, Serafima Semyenova, Andrey Vergun, Stephen O’Brien, and Alexey Ryskov

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Primary cultures of human colon cancer as a model to study cancer stem cells, Sergey Koshkin, Anna Danilova, Grigory Raskin, Nikolai Petrov, Olga Bajenova, Stephen J. O’Brien, Alexey Tomilin, and Elena Tolkunova

Context and Condition Dependent Plasticity in Sexual Signaling in Gray Treefrogs, Michael C. Kuczynski, Eben Gering, and Thomas Getty

Male Treefrogs in Low Condition Resume Signaling Faster Following Simulated Predator Attack, Michael C. Kuczynski, Levi Storks, Eben Gering, and Thomas Getty

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A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus), Markus H. Kuehn, Koren A. Lipsett, Marilyn Menotti-Raymond, S. Scott Whitmore, Todd E. Scheetz, Victor A. David, Stephen J. O'Brien, Zhongyuan Zhao, Jackie K. Jens, Elizabeth M. Snella, N. Matthew Ellinwood, and Gillian J. McLellan

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A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination, Gang Li, LaDeana W. Hillier, Robert A. Grahn, Aleksey V. Zimin, Victor A. David, Marilyn Menotti-Raymond, Rondo Middleton, Steven S. Hannah, Sher L. Hendrickson, Alexey Makunin, Stephen J. O'Brien, Patrick Minx, Richard K. Wilson, Leslie A. Lyons, Wesley C. Warren, and William J. Murphy

Antibiotics as a selective driver for conjugation dynamics, Allison J. Lopatkin, Shuqiang Huang, Robert P. Smith, Jaydeep K. Srimani, Tatyana A. Sysoeva, Sharon Bewick, David K. Karig, and Lingchong You

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Bone-Associated Gene Evolution and the Origin of Flight in Birds, Joao P. Machado, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, and Agostinho Antunes

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Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns, Joao P. Machado, Siby Philip, Emanuel Maldonado, Stephen J. O'Brien, and Warren E. Johnson

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Contrasting Origin of B Chromosomes in Two Cervids (Siberian Roe Deer and Grey Brocket Deer) Unravelled by Chromosome-Specific DNA Sequencing, Alexey I. Makunin, Ilya G. Kichigin, Denis M. Larkin, Patricia C. M. O'Brien, Malcolm A. Ferguson-Smith, Fengtang Yang, Anastasiya A. Proskuryakova, Nadezhda V. Vorobieva, Ekaterina N. Chernyaeva, Stephen J. O'Brien, Alexander S. Graphodatsky, and Vladimir Trifonov

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Mitochondrial genome of an Atlantic white shark (Carcharodon carcharias), Nicholas J. Marra, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Michael J. Stanhope, and Mahmood S. Shivji

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Otopathogenic Pseudomonas aeruginosa Enters and Survives Inside Macrophages, Rahul Mittal, Christopher V. Lisi, Hansi Kumari, M'hamed Grati, Patricia Blackwelder, Denise Yan, Chaitanya Jain, Kalai Mathee, Paulo H. Weckwerth, and Xue Zhong Liu

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De Novo Sequencing, Assembly and Analysis of Eight Different Transcriptomes from the Malayan Pangolin, Aini Mohamed Yusoff, Tze King Tan, Ranjeev Hari, Klaus-Peter Koepfli, Wei Yee Wee, Agostinho Antunes, Frankie Thomas Sitam, Jeffrine Japning Rovie-Ryan, Kayal Vizi Karuppannan, Guat Jah Wong, Leonard Lipovich, Wesley C. Warren, Stephen J. O'Brien, and Siew Woh Choo

Genetic Evidence for Contrasting Wetland and Savannah Habitat Specializations in Different Populations of Lions (Panthera leo), Andy E. Moore, Fenton P. D. (Woody) Cotterill, Christiaan W. Winterbach, Hanlie E. K. Winterbach, Agostinho Antunes, and Stephen J. O'Brien

Response to Comment by Faurby, Werdelin and Svenning, Stephen J. O'Brien, Klaus Peter Koepfli, Eduardo Eizirik, Warren Johnson, Carlos Driscoll, Agostinho Antunes, Anne Schmidt-Kuntzel, Laurie Marker, and Pavel Dobrynin

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Glycoside Hydrolases Family 20 (GH20) Represent Putative Virulence Factors That Are Shared by Animal Pathogenic Oomycetes, but Are Absent in Phytopathogens, Isabel Olivera, Katrina Fins, Sara Rodriguez, Sumayyah K. Abiff, Jaime Tartar, and Aurelien Tartar

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Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus, Andrew T. Ozga, Maria A. Nieves-Colon, Tanvi P. Honap, Krithivasan Sankaranarayanan, Courtney A. Hofman, George R. Milner, Cecil M. Lewis Jr., Anne C. Stone, and Christina Warinner

Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma, Andrew T. Ozga, Krithivasan Sankaranarayanan, Raul Y. Tito, Alexandra J. Obregon-Tito, Morris W. Foster, Gloria Tallbull, Paul Spicer, Christina G. Warinner, and Cecil M. Lewis Jr.

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Science Alive!: Connecting with Elementary Students through Science Exploration, Aarti Raja, Emily F. Schmitt Lavin, Tamara Gali, and Kaitlin Donovan

Koalas (Phascolarctos cinereus) from Queensland are genetically distinct from 2 populations in Victoria, Christina T. Ruiz-Rodriguez, Yasuko Ishida, Neil D. Murray, Stephen J. O'brien, Jennifer A.M. Graves, Alex D. Greenwood, and Alfred L. Roca

Developmental validation studies of epigenetic DNA methylation markers for the detection of blood, semen and saliva samples, Deborah S. B. S. Silva, Joana Antunes, Kuppareddi Balamurugan, George Duncan, Clarice S. Alho, and Bruce McCord

The Population Origins and Expansion of Feral Cats in Australia, Peter B.S. Spencer, Andrey A. Yurchenko, Victor A. David, Rachael Scott, Klaus Peter Koepfli, Carlos Driscoll, Stephen J. O'Brien, and Marilyn Menotti-Raymond

The Population Origins and Expansion of Feral Cats in Australia, Peter B. S. Spencer, Andrey A. Yurchenko, Victor A. David, Rachael Scott, Klaus-Peter Koepfli, Carlos Driscoll, Stephen J. O'Brien, and Marilyn Menotti-Raymond

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Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies, Ying Sun, Yu Huang, Xiaofeng Li, Carole C. Baldwin, Zhuocheng Zhou, Zhixiang Yan, Keith A. Crandall, Yong Zhang, Xiaomeng Zhao, Min Wang, Alex Wong, Chao Fang, Xinhui Zhang, Hai Huang, Jose V. Lopez, Kirk Kilfoyle, Yong Zhang, Guillermo Orti, Byrappa Venkatesh, and Qiong Shi

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Chromosomer: A Reference-Based Genome Arrangement Tool for Producing Draft Chromosome Sequences, Gaik Tamazian, Pavel Dobrynin, Ksenia Krasheninnikova, Aleksey Komissarov, Klaus-Peter Koepfli, and Stephen J. O'Brien

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PGD: a pangolin genome hub for the research community, Tze King Tan, Ka Yun Tan, Ranjeev Hari, Aini Mohamed Yusoff, Guat Jah Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mike Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O'Brien, and Siew Woh Choo

Continued Decline in Genetic Diversity Among Wild Cheetahs (Acinonyx jubatus) Without Further Loss of Semen Quality, Kimberly A. Terrell, Adrienne E. Crosier, David E. Wildt, Stephen J. O'Brien, Nicola M. Anthony, Laurie Marker, and Warren E. Johnson

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Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding, Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O'Brien, Michael C. Schatz, Tamas Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, and Laszlo Orban

Submissions from 2015

Effect of Carcinoembryonic Antigen Production by Colorectal Cancer Cells on Tumor Microenvironment and Cancer Progression, Olga Bajenova, I. Evsyukov, and Stephen J. O'Brien

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Gene Loss, Adaptive Evolution and the Co-Evolution of Plumage Coloration Genes with Opsins in Birds, Rui Borges, Imran Khan, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, and Agostinho Antunes

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Circumvention of Learning Increases Intoxication Efficacy of Nematicidal Engineered Bacteria, Olena R. Bracho, Cyril Mancherry, Evan Haskell, Christopher Blanar, and Robert P. Smith

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The First Whole Genome and Transcriptome of the Cinereous Vulture Reveals Adaptation in the Gastric and Immune Defense Systems and Possible Convergent Evolution between the Old and New World Vultures, Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, JeHoon Jun, HyeJin Lee, Alvin Chon, Junsu Ko, Jeremy Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O'Brien, Andrea Manica, Jong Bhak, and Woon Kee Paek

Horizontal Gene Transfer and Gene Dosage Drives Adaptation to Wood Colonization in a Tree Pathogen, Braham Dhillon, Nicolas Feau, Andrea Aerts, Stéphanie Beauseigle, Louis Bernier, Alex Copeland, Adam Foster, Navdeep Gill, Bernard Henrissat, Padmini Herath, Kurt LaButti, Anthony Levasseur, Erika Lindquist, Eline Majoor, Robin Ohm, Jasmyn Pangilinan, Amadeus Pribowo, John Saddler, Monique Sakalidis, Ronald P. de Vries, Igor Grigoriev, Stephen Goodwin, Philippe Tanguay, and Richard Hamelin

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Genomic Legacy of the African Cheetah, Acinonyx jubatus, Pavel Dobrynin, Shiping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergey Kliver, A. Schmidt-Kunzel, Klaus-Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel Garcia-Perez, Marc de Manuel, Ricardo Godinez, Aleksey Komissarov, Alexey Makunin, Vladimir Brukhin, Weilin Qiu, Long Zhou, Fang Li, Jian Yi, Carlos A. Driscoll, Agostinho Antunes, T. K. Oleksyk, Eduardo Eizirik, Polina Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, and Stephen J. O'Brien

Temperature-Dependent Variation in Self-Reported Contagious Yawning, Omar T. Eldakar, Melissa Dauzonne, Yana Prilutzkaya, Daniel Garcia, Carolyn Thadal, and Andrew C. Gallup

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Mixed Ancestry and Admixture in Kauai's Feral Chickens: Invasion of Domestic Genes into Ancient Red Junglefowl Reservoirs, Eben Gering, M. Johnsson, P. Willis, T. Getty, and D. Wright