Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

od Geistlinger, Ludwig, Csaba, Gergely, Zimmer, Ralf
izdano v BMC Bioinformatics (2016)

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

od Geistlinger, Ludwig, Csaba, Gergely, Küffner, Robert, Mulder, Nicola, Zimmer, Ralf
Izdano 2011

A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae

od Geistlinger, Ludwig, Csaba, Gergely, Dirmeier, Simon, Küffner, Robert, Zimmer, Ralf
Izdano 2013

Waldron et al. Reply to “Commentary on the HMP16SData Bioconductor Package”

od Waldron, Levi, Schiffer, Lucas, Azhar, Rimsha, Ramos, Marcel, Geistlinger, Ludwig, Segata, Nicola
izdano v Am J Epidemiol (2019)

Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data

od Oh, Sehyun, Geistlinger, Ludwig, Ramos, Marcel, Morgan, Martin, Waldron, Levi, Riester, Markus
izdano v JCO Clin Cancer Inform (2020)

Orchestrating a community-developed computational workshop and accompanying training materials

od Davis, Sean, Ramos, Marcel, Shepherd, Lori, Turaga, Nitesh, Geistlinger, Ludwig, Morgan, Martin T., Haibe-Kains, Benjamin, Waldron, Levi
izdano v F1000Res (2018)

HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor

od Schiffer, Lucas, Azhar, Rimsha, Shepherd, Lori, Ramos, Marcel, Geistlinger, Ludwig, Huttenhower, Curtis, Dowd, Jennifer B, Segata, Nicola, Waldron, Levi
izdano v Am J Epidemiol (2019)

Consensus on Molecular Subtypes of High-grade Serous Ovarian Carcinoma

od Chen, Gregory M, Kannan, Lavanya, Geistlinger, Ludwig, Kofia, Victor, Safikhani, Zhaleh, Gendoo, Deena MA, Parmigiani, Giovanni, Birrer, Michael, Haibe-Kains, Benjamin, Waldron, Levi
izdano v Clin Cancer Res (2018)

Multiomic Integration of Public Oncology Databases in Bioconductor

od Ramos, Marcel, Geistlinger, Ludwig, Oh, Sehyun, Schiffer, Lucas, Azhar, Rimsha, Kodali, Hanish, de Bruijn, Ino, Gao, Jianjiong, Carey, Vincent J., Morgan, Martin, Waldron, Levi
izdano v JCO Clin Cancer Inform (2020)

Toward a gold standard for benchmarking gene set enrichment analysis

od Geistlinger, Ludwig, Csaba, Gergely, Santarelli, Mara, Ramos, Marcel, Schiffer, Lucas, Turaga, Nitesh, Law, Charity, Davis, Sean, Carey, Vincent, Morgan, Martin, Zimmer, Ralf, Waldron, Levi
izdano v Brief Bioinform (2020)

Widespread modulation of gene expression by copy number variation in skeletal muscle

od Geistlinger, Ludwig, da Silva, Vinicius Henrique, Cesar, Aline Silva Mello, Tizioto, Polyana Cristine, Waldron, Levi, Zimmer, Ralf, Regitano, Luciana Correia de Almeida, Coutinho, Luiz Lehmann
izdano v Sci Rep (2018)

Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle

od da Silva, Vinicius Henrique, Regitano, Luciana Correia de Almeida, Geistlinger, Ludwig, Pértille, Fábio, Giachetto, Poliana Fernanda, Brassaloti, Ricardo Augusto, Morosini, Natália Silva, Zimmer, Ralf, Coutinho, Luiz Lehmann
izdano v PLoS One (2016)

A comprehensive manually-curated compendium of bovine transcription factors

od de Souza, Marcela M., Zerlotini, Adhemar, Geistlinger, Ludwig, Tizioto, Polyana C., Taylor, Jeremy F., Rocha, Marina I. P., Diniz, Wellison J. S., Coutinho, Luiz L., Regitano, Luciana C. A.
izdano v Sci Rep (2018)

Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study

od Beghini, Francesco, Renson, Audrey, Zolnik, Christine P., Geistlinger, Ludwig, Usyk, Mykhaylo, Moody, Thomas U., Thorpe, Lorna, Dowd, Jennifer B., Burk, Robert, Segata, Nicola, Jones, Heidi E., Waldron, Levi
izdano v Ann Epidemiol (2019)

Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum

od Gieger, Christian, Geistlinger, Ludwig, Altmaier, Elisabeth, Hrabé de Angelis, Martin, Kronenberg, Florian, Meitinger, Thomas, Mewes, Hans-Werner, Wichmann, H.-Erich, Weinberger, Klaus M., Adamski, Jerzy, Illig, Thomas, Suhre, Karsten
Izdano 2008

Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle

od Diniz, Wellison J. S., Mazzoni, Gianluca, Coutinho, Luiz L., Banerjee, Priyanka, Geistlinger, Ludwig, Cesar, Aline S. M., Bertolini, Francesca, Afonso, Juliana, de Oliveira, Priscila S. N., Tizioto, Polyana C., Kadarmideen, Haja N., Regitano, Luciana C. A.
izdano v Front Genet (2019)

Orchestrating Single-Cell Analysis with Bioconductor

od Amezquita, Robert A., Lun, Aaron T. L., Becht, Etienne, Carey, Vince J., Carpp, Lindsay N., Geistlinger, Ludwig, Marini, Federico, Rue-Albrecht, Kevin, Risso, Davide, Soneson, Charlotte, Waldron, Levi, Pagès, Hervé, Smith, Mike L., Huber, Wolfgang, Morgan, Martin, Gottardo, Raphael, Hicks, Stephanie C.
izdano v Nat Methods (2019)

SIMON: Open-Source Knowledge Discovery Platform

od Tomic, Adriana, Tomic, Ivan, Waldron, Levi, Geistlinger, Ludwig, Kuhn, Max, Spreng, Rachel L., Dahora, Lindsay C., Seaton, Kelly E., Tomaras, Georgia, Hill, Jennifer, Duggal, Niharika A., Pollock, Ross D., Lazarus, Norman R., Harridge, Stephen D.R., Lord, Janet M., Khatri, Purvesh, Pollard, Andrew J., Davis, Mark M.
izdano v Patterns (N Y) (2021)

Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set

od Kurome, Mayuko, Geistlinger, Ludwig, Kessler, Barbara, Zakhartchenko, Valeri, Klymiuk, Nikolai, Wuensch, Annegret, Richter, Anne, Baehr, Andrea, Kraehe, Katrin, Burkhardt, Katinka, Flisikowski, Krzysztof, Flisikowska, Tatiana, Merkl, Claudia, Landmann, Martina, Durkovic, Marina, Tschukes, Alexander, Kraner, Simone, Schindelhauer, Dirk, Petri, Tobias, Kind, Alexander, Nagashima, Hiroshi, Schnieke, Angelika, Zimmer, Ralf, Wolf, Eckhard
Izdano 2013

Multi-omic analysis of subtype evolution and heterogeneity in high-grade serous ovarian carcinoma

od Geistlinger, Ludwig, Oh, Sehyun, Ramos, Marcel, Schiffer, Lucas, LaRue, Rebecca S., Henzler, Christine M., Munro, Sarah A., Daughters, Claire, Nelson, Andrew C., Winterhoff, Boris J., Chang, Zenas, Talukdar, Shobhana, Shetty, Mihir, Mullaney, Sally A., Morgan, Martin, Parmigiani, Giovanni, Birrer, Michael J., Qin, Li-Xuan, Riester, Markus, Starr, Timothy K., Waldron, Levi
izdano v Cancer Res (2020)