Genomics and Bioinformatics

Genomics and Bioinformatics Research

Projects

Publications

• “Multi-omics data integration by generative adversarial network”, Wei Zhang, Ph.D., Khandakar Tanvir Ahmed, Ph.D., Jiao Sun, Ph.D., Sze Cheng, Ph.D., Jeongsik Yong, Ph.D., Bioinformatics btab608: Aug, 2021
• “In silico model for miRNA-mediated regulatory network in cancer”, Wei Zhang, Ph.D., Khandakar Tanvir Ahmed, Ph.D., Jiao Sun, Ph.D., William Chen, Ph.D., Irene Martinez, Ph.D., Sze Cheng, Ph.D., Wencai Zhang, Ph.D., Jeongsik Yong, Ph.D., Briefings in Bioinformatics bbab264: Jul, 2021
• “PumaPlex100: an expanded tool for puma SNP genotyping with low-yield DNA”, Robert Fitak, Ph.D., John A. Erwin, Ph.D., Melanie Culver, Ph.D., Conservation Genetics Resources 13, 341–343: Apr, 2021
• “Exopolysaccharide Anchoring Creates an Extreme Resistance to Sedimentation”, Sean Moore, Ph.D., Nickolas G. Kessler, Ph.D., David M. Caraballo Delgado, Ph.D., Neel K. Shah, Ph.D., Jeff A. Dickinson, Ph.D., Journal of Bacteriology 203(11), e00023-21: May, 2021
• “Pulmonary Microbiome of Patients Receiving Mechanical Ventilation: Changes Over Time”, ., Shibu Yooseph, Ph.D., Mary Lou Sole, Ph.D., RN, CCNS, CNL, Steven Talbert, Ph.D., RN, Bassam Abomoelak, Ph.D., MT, Chirajyoti Deb, Ph.D., Kimberly Paige Rathburn, BSN, RN, Daleen Penoyer, Ph.D., RN, CCRP, Aurea Middleton, BSN, RN, & Devendra Mehta, MBBS, MSc, MRCP, American Journal of Critical Care 30 (2): 128–132: Mar, 2021
• “Peroxidized Linoleic Acid, 13-HPODE, Alters Gene Expression Profile in Intestinal Epithelial Cells”, ., Anna Forsman, Ph.D., Shibu Yooseph, Ph.D., Nisreen Faizo, Ph.D., Chandrakala Aluganti Narasimhulu, Ph.D., & Sampath Parthasarathy, Ph.D., Foods 10(2), 314: Feb, 2021
• “Bacterial community structure alterations within the colorectal cancer gut microbiome”, ., Shibu Yooseph, Ph.D., Mark Loftus, Ph.D., & Sayf Al-Deen Hassouneh, Ph.D., , BMC Microbiology 21, 98: Mar, 2021
• “Identification of Nasal Gammaproteobacteria with Potent Activity against Staphylococcus aureus: Novel Insights into the "Noncarrier" State”, ., Anna Forsman, Ph.D., Shibu Yooseph, Ph.D., Amy L. Cole, Ph.D., Meera Sundar, Ph.D., Ana Lopez, Ph.D., Alexander M. Cole, Ph.D., mSphere 6(1):e01015-20: Jan, 2021
• “Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia”, ., Michelle Gaither, Ph.D., O. Selma Klanten, Ph.D., Samuel Greaves, Ph.D., Kade Mills, Ph.D., Kristine O’Keeffe, Ph.D., John Turnbull, Ph.D., Rob McKinnon, Ph.D., David J. Booth, Ph.D., PloS One: Dec, 2020
• “Bacterial associations in the healthy human gut microbiome across populations”, Scientific Reports: Sep, 2020
• “Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research”, ., Michelle Gaither, Ph.D., Cynthia Riginos, Ph.D., Eric D. Crandall, Ph.D., Libby Liggins, Ph.D., Rodney B. Ewing, Ph.D., Christopher Meyer, Ph.D., Kimberly R. Andrews, Ph.D., Peter T. Euclide, Ph.D., Benjamin M. Titus, Ph.D., Nina Overgaard Therkildsen, Ph.D., Antonia Salces-Castellano, Ph.D., Lucy C. Stewart, Ph.D., Robert J. Toonen, Ph.D., John Deck, Ph.D., Molecular Ecology Resources 20 (6), 1458-1469: Oct, 2020
• “Does color matter? Molecular and ecological divergence in four sympatric color morphs of a coral reef fish”, ., Michelle Gaither, Ph.D., Darren J. Coker, Ph.D., Samuel Greaves, Ph.D., Fatih Sarigol, Ph.D., Samuel D. Payet, Ph.D., Veronica Chaidez, Ph.D., Tane H. Sinclair-Taylor, Ph.D., Joseph D. DiBattista, Ph.D., Michael L. Berumen, Ph.D., Ecology and Evolution 10 (18), 9663-9681: Sep, 2020
• “Pulse magnetization elicits differential gene expression in the central nervous system of the Caribbean spiny lobster, Panulirus argus”, ., Robert Fitak, Ph.D., David A. Ernst, Ph.D., Manfred Schmidt, Ph.D., Charles D. Derby, Ph.D., Sönke Johnsen, Ph.D., & Kenneth J. Lohmann, Ph.D., Journal of Comparative Physiology A 206, 725–74: Jun, 2020
• “Symbiotic magnetic sensing: raising evidence and beyond”, Robert Fitak, Ph.D., Eviatar Natan, Ph.D., Yuval Werber, Ph.D., Yoni Vortman, Ph.D., Philosophical Transactions of the Royal Society B 37520190595: Aug, 2020
• “Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula”, ., Yan Solihin, Ph.D., Yuanchao Xu, Ph.D., Xipeng Shen, Ph.D., Ecology and Evolution pp. 987-1000: Apr, 2020
• “Gray whales strand more often on days with increased levels of atmospheric radio-frequency noise”, Robert Fitak, Ph.D., Jesse Granger, Ph.D., Lucianne Walkowicz, Ph.D., Sönke Johnsen, Ph.D., Current Biology 30(4):R155-R156: Feb, 2020
• “Genomic signatures of domestication in Old World camels”, Robert Fitak, Ph.D., Elmira Mohandesan, Ph.D., Jukka Corander, Ph.D., Adiya Yadamsuren, Ph.D., Battsetseg Chuluunbat, Ph.D., Omer Abdelhadi, Ph.D., Abdul Raziq, Ph.D., Peter Nagy, Ph.D., Chris Walzer, Ph.D., Bernard Faye, Ph.D., Pamela Anna Burger, Ph.D., Communications Biology 3, 316: Jun, 2020
• “The physiology of rapid ecological specialization: A look at the Midas cichlids”, ., Michelle Gaither, Ph.D., Samuel Greaves, Ph.D., Pavithiran Amirthalingam, Ph.D., Molecular Ecology 29(7), 1215-1218: Mar, 2020
• “Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin”, Robert Fitak, Ph.D., Carlos Taboada, Ph.D., Andrés E. Brunetti, Ph.D., Mariana L. Lyra, Ph.D., Ana Faigón Soverna, Ph.D., Santiago R. Ron, Ph.D., María G. Lagorio, Ph.D., Célio F. B. Haddad, Ph.D., Norberto P. Lopes, Ph.D., Sönke Johnsen, Ph.D., Julián Faivovich, Ph.D., Lucía B. Chemes, Ph.D., Sara E. Bari, Ph.D., Proceedings of the National Academy of Sciences 117 (31) 18574-18581: Jul, 2020
• “De Novo Assembly and Annotation from Parental and F1 Puma Genomes of the Florida Panther Genetic Restoration Program”, Robert Fitak, Ph.D., Alexander Ochoa, Ph.D., David P Onorato, Ph.D., Melody E Roelke-Parker, Ph.D., Melanie Culver, Ph.D., G3 Genes|Genomes|Genetics 9(11), 3531-3536: Nov, 2019