| MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs DH Huson, B Albrecht, C Bağcı, I Bessarab, A Gorska, D Jolic, ... Biology direct 13, 1-17, 2018 | 182 | 2018 |
| DIAMOND+ MEGAN: fast and easy taxonomic and functional analysis of short and long microbiome sequences C Bağcı, S Patz, DH Huson Current protocols 1 (3), e59, 2021 | 104 | 2021 |
| Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data K Arumugam, C Bağcı, I Bessarab, S Beier, B Buchfink, A Górska, G Qiu, ... Microbiome 7, 1-13, 2019 | 78 | 2019 |
| The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains … S Esquivel-Elizondo, C Bağcı, M Temovska, BS Jeon, I Bessarab, ... Frontiers in microbiology 11, 594524, 2021 | 73 | 2021 |
| Computational Prediction of MicroRNAs from Toxoplasma Gondii Potentially Regulating the Hosts’ Gene Expression MD Saçar, C Bağcı, J Allmer Genomics, Proteomics and Bioinformatics 12 (5), 228-238, 2014 | 50 | 2014 |
| Methods in molecular biology ZL Dlamini, Z Mbita, D Bates Humana Press Inc., 2016 | 40* | 2016 |
| Introduction to the analysis of environmental sequences: metagenomics with MEGAN C Bağcı, S Beier, A Górska, DH Huson Evolutionary genomics: statistical and computational methods, 591-604, 2019 | 37 | 2019 |
| One step forward, two steps back; xeno-microRNAs reported in breast milk are artifacts C Bağcı, J Allmer PloS one 11 (1), e0145065, 2016 | 34 | 2016 |
| Using AnnoTree to get more assignments, faster, in DIAMOND+ MEGAN microbiome analysis A Gautam, H Felderhoff, C Bağci, DH Huson Msystems 7 (1), e01408-21, 2022 | 31 | 2022 |
| Differential Expression of Toxoplasma gondii MicroRNAs in Murine and Human Hosts MD Saçar Demirci, C Bağcı, J Allmer Non-coding RNAs and inter-kingdom communication, 143-159, 2016 | 13 | 2016 |
| Microbial phylogenetic context using phylogenetic outlines C Bagci, D Bryant, B Cetinkaya, DH Huson Genome biology and evolution 13 (9), evab213, 2021 | 9 | 2021 |
| MAIRA-real-time taxonomic and functional analysis of long reads on a laptop B Albrecht, C Bağcı, DH Huson BMC bioinformatics 21, 1-12, 2020 | 9 | 2020 |
| Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data. Microbiome 7, 61 K Arumugam, C Bağcı, I Bessarab, S Beier, B Buchfink, A Górska, G Qiu, ... | 5 | 2019 |
| BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes C Bağcı, M Nuhamunada, H Goyat, C Ladanyi, L Sehnal, K Blin, ... Nucleic acids research 53 (D1), D618-D624, 2025 | 4 | 2025 |
| One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts.. 2016;(1): e0145065| C Bağcı, J Allmer PLoS One 11, 0 | 4 | |
| Removing contamination from genomic sequences based on vector reference libraries C Bagci, J Allmer 2012 7th international symposium on health informatics and bioinformatics …, 2012 | 2 | 2012 |
| Efficient Algorithms and Pipelines for Microbiome Analysis C Bağcı Universität Tübingen, 2025 | | 2025 |
| Strong pairwise Interactions do not Drive Interactions in a Plant Leaf Associated Microbial Community F Hoehn, C Bagci, V Chaudhry, P Stincone, M Mahmoudi, L Berg, E Klenk, ... bioRxiv, 2024.05. 22.595276, 2024 | | 2024 |
| MAIRA: Protein-based Analysis of MinION Reads on a Laptop C Bağcı, B Albrecht, DH Huson Metagenomic Data Analysis, 223-234, 2023 | | 2023 |
| Analysis of Large-Scale Microbiome Sequencing Datasets on BinAC S Patz, C Bağcı, M Balvočiūte, B Albrecht, BB Xavier, BS Jeon, ... Book of Abstracts, 37, 2019 | | 2019 |
