Search Results - "Topcuoglu, Begum D"

Long-term forest soil warming alters microbial communities in temperate forest soils by DeAngelis, Kristen M, Pold, Grace, Topçuoğlu, Begüm D, van Diepen, Linda T A, Varney, Rebecca M, Blanchard, Jeffrey L, Melillo, Jerry, Frey, Serita D

“…Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing…”
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Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer by Topçuoğlu, Begüm D, Meydan, Cem, Nguyen, Tran B, Lang, Susan Q, Holden, James F

“…Hyperthermophilic methanogens are often H limited in hot subseafloor environments, and their survival may be due in part to physiological adaptations to low H…”
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Formate hydrogenlyase and formate secretion ameliorate H 2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae by Topçuoğlu, Begüm D, Meydan, Cem, Orellana, Roberto, Holden, James F

“…Some hyperthermophilic heterotrophs in the genus Thermococcus produce H in the absence of S° and have up to seven hydrogenases, but their combined…”
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Ten simple rules to increase computational skills among biologists with Code Clubs by Hagan, Ada K, Lesniak, Nicholas A, Balunas, Marcy J, Bishop, Lucas, Close, William L, Doherty, Matthew D, Elmore, Amanda G, Flynn, Kaitlin J, Hannigan, Geoffrey D, Koumpouras, Charlie C, Jenior, Matthew L, Kozik, Ariangela J, McBride, Kathryn, Rifkin, Samara B, Stough, Joshua M A, Sovacool, Kelly L, Sze, Marc A, Tomkovich, Sarah, Topcuoglu, Begum D, Schloss, Patrick D

“…Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, United States of America Affiliation: Department of Microbiology and Immunology,…”
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A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems by Topçuoğlu, Begüm D, Lesniak, Nicholas A, Ruffin, 4th, Mack T, Wiens, Jenna, Schloss, Patrick D

“…Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as…”
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A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer by Armour, Courtney R, Topçuoğlu, Begüm D, Garretto, Andrea, Schloss, Patrick D

“…Colorectal cancer is a common and deadly disease in the United States accounting for over 50,000 deaths in 2020. This progressive disease is highly preventable…”
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Women Are Underrepresented and Receive Differential Outcomes at ASM Journals: a Six-Year Retrospective Analysis by Hagan, Ada K, Topçuoğlu, Begüm D, Gregory, Mia E, Barton, Hazel A, Schloss, Patrick D

“…Despite 50% of biology Ph.D. graduates being women, the number of women that advance in academia decreases at each level (e.g., from graduate to postdoctorate…”
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Experimental investigation on the controls of clumped isotopologue and hydrogen isotope ratios in microbial methane by Gruen, Danielle S., Wang, David T., Könneke, Martin, Topçuoğlu, Begüm D., Stewart, Lucy C., Goldhammer, Tobias, Holden, James F., Hinrichs, Kai-Uwe, Ono, Shuhei

“…The abundance of methane isotopologues with two rare isotopes (e.g., 13CH3D) has been proposed as a tool to estimate the temperature at which methane is formed…”
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Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure by Sze, Marc A, Topçuoğlu, Begüm D, Lesniak, Nicholas A, Ruffin, 4th, Mack T, Schloss, Patrick D

“…Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others…”
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Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents by Topçuoğlu, Begüm D, Stewart, Lucy C, Morrison, Hilary G, Butterfield, David A, Huber, Julie A, Holden, James F

“…Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly…”
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Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities by Fortunato, Caroline S, Butterfield, David A, Larson, Benjamin, Lawrence-Slavas, Noah, Algar, Christopher K, Zeigler Allen, Lisa, Holden, James F, Proskurowski, Giora, Reddington, Emily, Stewart, Lucy C, Topçuoğlu, Begüm D, Vallino, Joseph J, Huber, Julie A

“…Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this…”
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Machine learning classification by fitting amplicon sequences to existing OTUs by Armour, Courtney R, Sovacool, Kelly L, Close, William L, Topçuoğlu, Begüm D, Wiens, Jenna, Schloss, Patrick D

“…The ability to use 16S rRNA gene sequence data to train machine learning classification models offers the opportunity to diagnose patients based on the…”
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Erratum for Hagan et al., "Women Are Underrepresented and Receive Differential Outcomes at ASM Journals: a Six-Year Retrospective Analysis" by Hagan, Ada K, Topçuoğlu, Begüm D, Gregory, Mia E, Barton, Hazel A, Schloss, Patrick D

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Vaccine Hyporesponse Induced by Individual Antibiotic Treatment in Mice and Non-Human Primates Is Diminished upon Recovery of the Gut Microbiome by Swaminathan, Gokul, Citron, Michael, Xiao, Jianying, Norton, James E., Reens, Abigail L., Topçuoğlu, Begüm D., Maritz, Julia M., Lee, Keun-Joong, Freed, Daniel C., Weber, Teresa M., White, Cory H., Kadam, Mahika, Spofford, Erin, Bryant-Hall, Erin, Salituro, Gino, Kommineni, Sushma, Liang, Xue, Danilchanka, Olga, Fontenot, Jane A., Woelk, Christopher H., Gutierrez, Dario A., Hazuda, Daria J., Hannigan, Geoffrey D.

“…Emerging evidence demonstrates a connection between microbiome composition and suboptimal response to vaccines (vaccine hyporesponse). Harnessing the…”
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Very early life microbiome and metabolome correlates with primary vaccination variability in children by Shaffer, Michael, Best, Katharine, Tang, Catherine, Liang, Xue, Schulz, Steven, Gonzalez, Eduardo, White, Cory H, Wyche, Thomas P, Kang, John, Wesseling, Hendrik, Topçuoğlu, Begüm D, Cairns, Thomas, Sana, Theodore R, Kaufhold, Robin M, Maritz, Julia M, Woelk, Christopher H, Swaminathan, Gokul, Norton, Jr, James E, Pichichero, Michael E

“…We show that simultaneous study of stool and nasopharyngeal microbiome reveals divergent timing and patterns of maturation, suggesting that local mucosal…”
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Lower hydrogen flux leads to larger carbon isotopic fractionation of methane and biomarkers during hydrogenotrophic methanogenesis by Nguyen, T.B., Topçuoğlu, B.D., Holden, J.F., LaRowe, D.E., Lang, S.Q.

“…The isotopic composition of lipid biomarkers and biomass in sedimentary environments are widely used to infer microbial metabolisms and constrain carbon…”
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Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae by Topçuoğlu, Begüm D., Meydan, Cem, Orellana, Roberto, Holden, James F.

“…Summary Some hyperthermophilic heterotrophs in the genus Thermococcus produce H2 in the absence of S° and have up to seven hydrogenases, but their combined…”
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mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines by Topçuoğlu, Begüm D, Lapp, Zena, Sovacool, Kelly L, Snitkin, Evan, Wiens, Jenna, Schloss, Patrick D

“…Machine learning (ML) for classification and prediction based on a set of features is used to make decisions in healthcare, economics, criminal justice and…”
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