User profiles for Begüm D. Topçuoğlu

Begüm D. Topçuoğlu

Bristol Myers Squibb
Verified email at bms.com
Cited by 2039

[HTML][HTML] Long-term forest soil warming alters microbial communities in temperate forest soils

KM DeAngelis, G Pold, BD Topçuoğlu… - Frontiers in …, 2015 - frontiersin.org
Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how
climate warming will affect microbial communities. Three ongoing field studies at the Harvard …

A framework for effective application of machine learning to microbiome-based classification problems

BD Topçuoğlu, NA Lesniak, MT Ruffin IV, J Wiens… - MBio, 2020 - Am Soc Microbiol
ABSTRACT 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 …

Experimental investigation on the controls of clumped isotopologue and hydrogen isotope ratios in microbial methane

DS Gruen, DT Wang, M Könneke, BD Topçuoğlu… - … et Cosmochimica Acta, 2018 - Elsevier
… barkeri using D-spiked water or D-… 3 D values of product methane only weakly correlate
with the D/H ratio of medium water. Our experimental results demonstrate that low Δ 13 CH 3 D

Women are underrepresented and receive differential outcomes at ASM journals: a six-year retrospective analysis

AK Hagan, BD Topçuoğlu, ME Gregory, HA Barton… - MBio, 2020 - Am Soc Microbiol
Despite 50% of biology Ph.D. graduates being women, the number of women that advance
in academia decreases at each level (eg, from graduate to postdoctorate to tenure track). …

[HTML][HTML] mikropml: user-friendly R package for supervised machine learning pipelines

BD Topçuoğlu, Z Lapp, KL Sovacool… - Journal of open …, 2021 - ncbi.nlm.nih.gov
Machine learning (ML) for classification and prediction based on a set of features is used to
make decisions in healthcare, economics, criminal justice and more. However, implementing …

Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure

MA Sze, BD Topçuoğlu, NA Lesniak, MT Ruffin IV… - MBio, 2019 - Am Soc Microbiol
Colonic bacterial populations are thought to have a role in the development of colorectal
cancer with some protecting against inflammation and others exacerbating inflammation. Short-…

[HTML][HTML] Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents

BD Topçuoğlu, LC Stewart, HG Morrison… - Frontiers in …, 2016 - frontiersin.org
Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth
constraints and dependence on H 2 syntrophy in situ are poorly understood. Between 2012 …

Very early life microbiome and metabolome correlates with primary vaccination variability in children

…, TP Wyche, J Kang, H Wesseling, BD Topçuoğlu… - Msystems, 2023 - Am Soc Microbiol
Despite multiple vaccine doses early in life, a substantial proportion of infants do not mount
protective responses. In this study, we followed a cohort of children over the first 2 years of life…

Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and …

BD Topçuoğlu, C Meydan, TB Nguyen… - Applied and …, 2019 - Am Soc Microbiol
Hyperthermophilic methanogens are often H 2 limited in hot subseafloor environments, and
their survival may be due in part to physiological adaptations to low H 2 conditions and …

A goldilocks principle for the gut microbiome: taxonomic resolution matters for microbiome-based classification of colorectal cancer

CR Armour, BD Topçuoğlu, A Garretto, PD Schloss - MBio, 2022 - Am Soc Microbiol
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 with early detection …