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Permanent URI for this collectionhttps://hdl.handle.net/11443/932

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Author: search.filters.author.Sezerman, UgurHas files: No

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Now showing 1 - 4 of 4
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    The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report
    (BMC, 2016-01-01) Chernomoretz, Ariel; Stolovitzky, Gustavo; Labaj, Pawel P.; Graf, Alexandra B.; Darling, Aaron; Burke, Catherine; Noushmehr, Houtan; Moraes, Milton Ozorio; Dias-Neto, Emmanuel; Guo, Yongli; Xie, Zhi; Lee, Patrick; Shi, Leming; Ruiz-Perez, Carlos A.; Mercedes Zambrano, Maria; Siam, Rania; Ouf, Amged; Richard, Hugues; Lafontaine, Ingrid; Wieler, Lothar H.; Semmler, Torsten; Ahmed, Niyaz; Prithi-viraj, Bharath; Nedunuri, Narasimha; Mehr, Shaadi; Banihashemi, Kambiz; Lista, Florigio; Anselmo, Anna; Suzuki, Haruo; Kuroda, Makoto; Yamashita, Riu; Sato, Yukoto; Kaminuma, Eli; Alpuche Aranda, Celia M.; Martinez, Jesus; Dada, Christopher; Dybwad, Marius; Oliveira, Manuela; Schuster, Stephan; Siwo, Geoffrey H.; Jang, Soojin; Seo, Sung Chul; Hwang, Sung Ho; Ossowski, Stephan; Bezdan, Daniela; Chaker, Salama; Chatziefthimiou, Aspassia D.; Udekwu, Klas; Liungdahl, Per; Sezerman, Ugur; Meydan, Cem; Elhaik, Eran; Gonnet, Gaston; Schriml, Lynn M.; Mongodin, Emmanuel; Huttenhower, Curtis; Gilbert, Jack; Mason, Christopher E.; Eisen, Jonathan; Hirschberg, David; Hernandez, Mark; Consortium, MetaSU.B. Int
    The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.
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    Investigating the role of common and rare variants in multiplex multiple sclerosis families reveals an increased burden of common risk variation
    (NATURE PORTFOLIO, 2022-01-01) Everest, Elif; Ahangari, Mohammad; Uygunoglu, Ugur; Tutuncu, Melih; Bulbul, Alper; Saip, Sabahattin; Duman, Taskin; Sezerman, Ugur; Reich, Daniel S.; Riley, Brien P.; Siva, Aksel; Turanli, Eda Tahir
    Many multiple sclerosis (MS)-associated common risk variants as well as candidate low-frequency and rare variants have been identified
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    Differential gene expression analysis of human cumulus cells
    (KOREAN SOC REPRODUCTIVE MEDICINE, 2019-01-01) Demiray, Sirin Bakti; Goker, Ege Nazan Tavmergen; Tavmergen, Erol; Yilmaz, Ozlem; Calimlioglu, Nilufer; Soykam, Huseyin Okan; Oktem, Gulperi; Sezerman, Ugur
    Objective: This study was performed to explore the possibility that each oocyte and its surrounding cumulus cells might have different genetic expression patterns that could affect human reproduction. Methods: Differential gene expression analysis was performed for 10 clusters of cumulus cells obtained from 10 cumulus-oocyte complexes from 10 patients. Same procedures related to oocyte maturation, microinjection, and microarray analyses were performed for each group of cumulus cells. Two differential gene expression analyses were performed: one for the outcome of clinical pregnancy and one for the outcome of live birth. Results: Significant genes resulting from these analyses were selected and the top 20 affected pathways in each group were analyzed. Circadian entrainment is determined to be the most affected pathway for clinical pregnancy, and proteoglycans in cancer pathway is the most affected pathway for live birth. Circadian entrainment is also amongst the 12 pathways that are found to be in top 20 affected pathways for both outcomes, and has both lowest p-value and highest number of times found count. Conclusion: Although further confirmatory studies are necessary, findings of this study suggest that these pathways, especially circadian entrainment in cumulus cells, may be essential for embryo development and pregnancy.
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    Base-excess chloride
    (PUBLIC LIBRARY SCIENCE, 2021-01-01) Gucyetmez, Bulent; Tuzuner, Filiz; Atalan, Hakan Korkut; Sezerman, Ugur; Gucyetmez, Kaan; Telci, Lutfi
    To practically determine the effect of chloride (Cl) on the acid-base status, four approaches are currently used: accepted ranges of serum Cl values