| Orchestrating single-cell analysis with Bioconductor RA Amezquita, ATL Lun, E Becht, VJ Carey, LN Carpp, L Geistlinger, ... Nature methods 17 (2), 137-145, 2020 | 1042 | 2020 |
| Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals F Asnicar, SE Berry, AM Valdes, LH Nguyen, G Piccinno, DA Drew, ... Nature medicine 27 (2), 321-332, 2021 | 995 | 2021 |
| Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum C Gieger, L Geistlinger, E Altmaier, M Hrabé de Angelis, F Kronenberg, ... PLoS genetics 4 (11), e1000282, 2008 | 894 | 2008 |
| Reporting guidelines for human microbiome research: the STORMS checklist C Mirzayi, A Renson, Genomic Standards Consortium, ... Nature medicine 27 (11), 1885-1892, 2021 | 416 | 2021 |
| Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma GM Chen, L Kannan, L Geistlinger, V Kofia, Z Safikhani, D Gendoo, ... Clinical Cancer Research 24 (20), 5037-5047, 2018 | 172 | 2018 |
| Toward a gold standard for benchmarking gene set enrichment analysis L Geistlinger, G Csaba, M Santarelli, M Ramos, L Schiffer, N Turaga, ... Briefings in bioinformatics 22 (1), 545-556, 2021 | 161 | 2021 |
| Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space MC Schatz, AA Philippakis, E Afgan, E Banks, VJ Carey, RJ Carroll, ... Cell Genomics 2 (1), 2022 | 144 | 2022 |
| Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma L Geistlinger, S Oh, M Ramos, L Schiffer, RS LaRue, CM Henzler, ... Cancer research 80 (20), 4335-4345, 2020 | 121 | 2020 |
| Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set M Kurome, L Geistlinger, B Kessler, V Zakhartchenko, N Klymiuk, ... BMC biotechnology 13 (1), 43, 2013 | 121 | 2013 |
| Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set-& network-based enrichment analysis L Geistlinger, G Csaba, R Zimmer BMC bioinformatics 17 (1), 45, 2016 | 108 | 2016 |
| Multiomic integration of public oncology databases in bioconductor M Ramos, L Geistlinger, S Oh, L Schiffer, R Azhar, H Kodali, I de Bruijn, ... JCO clinical cancer informatics 1, 958-971, 2020 | 100 | 2020 |
| Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling P Cadinu, KN Sivanathan, A Misra, RJ Xu, D Mangani, E Yang, JM Rone, ... Cell 187 (8), 2010-2028. e30, 2024 | 90 | 2024 |
| From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems L Geistlinger, G Csaba, R Küffner, N Mulder, R Zimmer Bioinformatics 27 (13), i366-i373, 2011 | 89 | 2011 |
| A platform for the biomedical application of large language models S Lobentanzer, S Feng, N Bruderer, A Maier, C Wang, J Baumbach, ... Nature biotechnology 43 (2), 166-169, 2025 | 64 | 2025 |
| Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution BR Watson, B Paul, RU Rahman, L Amir-Zilberstein, Å Segerstolpe, ... Nature Communications 16 (1), 319, 2025 | 62 | 2025 |
| Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle VH Silva, LCA Regitano, L Geistlinger, F Pértille, PF Giachetto, ... PloS one 11 (6), e0157711, 2016 | 61 | 2016 |
| Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits ASM Cesar, LCA Regitano, JM Reecy, MD Poleti, PSN Oliveira, ... BMC genomics 19 (1), 499, 2018 | 57 | 2018 |
| Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study F Beghini, A Renson, CP Zolnik, L Geistlinger, M Usyk, TU Moody, ... Annals of epidemiology 34, 18-25. e3, 2019 | 44 | 2019 |
| HMP16SData: efficient access to the Human Microbiome Project through Bioconductor L Schiffer, R Azhar, L Shepherd, M Ramos, L Geistlinger, C Huttenhower, ... Am J Epidemiol 188 (6), 1023-1026, 2018 | 40 | 2018 |
| CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes V da Silva, M Ramos, M Groenen, R Crooijmans, A Johansson, ... Bioinformatics, 2019 | 37 | 2019 |
