Ludwig Geistlinger, PhD

Ludwig Geistlinger, PhD

Senior Computational Biologist

Center for Computational Biomedicine

Harvard Medical School

Dr. Ludwig Geistlinger is a Computational Biologist at the Center of Computational Biomedicine, taking a leading role in its mission to support the broad use of leading-edge computational and analytic methods at Harvard Medical School. Prior to his work at CCB, Dr. Geistlinger completed a PhD in bioinformatics focusing on network-based analysis of gene expression data at the University of Munich, Germany; and a post-doctoral fellowship at the University of São Paulo, Brazil, where he analyzed the effects of structural genome variation on gene expression. He then held a post-doctoral research position in the lab of Levi Waldron at the School of Public Health of the City University of New York, where he developed integrative and scalable solutions for cancer genomics in R/Bioconductor. Dr. Geistlinger’s research interests are in computational biology and biostatistics, with applications in single-cell and bulk RNA-seq analysis, gene set and network enrichment analysis, copy number variation analysis, human microbiome analysis, and multi-omic analysis in the cancer genomics field.

  • GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases

    Authors: Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S.

    Nat Commun. 2022

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  • Reporting Guidelines for Human Microbiome Research: the STORMS checklist

    Authors: Mirzayi C, Renson A; Genomic Standards Consortium; Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L.

    Nat Med. 2021

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  • Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

    Authors: Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, Leeming E, Gibson R, Le Roy C, Khatib HA, Francis L, Mazidi M, Mompeo O, Valles-Colomer M, Tett A, Beghini F, Dubois L, Bazzani D, Thomas AM, Mirzayi C, Khleborodova A, Oh S, Hine R, Bonnett C, Capdevila J, Danzanvilliers S, Giordano F, Geistlinger L, Waldron L, Davies R, Hadjigeorgiou G, Wolf J, Ordovás JM, Gardner C, Franks PW, Chan AT, Huttenhower C, Spector TD, Segata N.

    Nat Med. 2021

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  • Toward a gold standard for benchmarking gene set enrichment analysis

    Authors: Geistlinger L, Csaba G, Santarelli M, Ramos M, Schiffer L, Turaga N, Law C, Davis S, Carey V, Morgan M, Zimmer R, Waldron L.

    Brief Bioinform. 2021

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  • Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma

    Authors: Geistlinger L, Oh S, Ramos M, Schiffer L, LaRue RS, Henzler CM, Munro SA, Daughters C, Nelson AC, Winterhoff BJ, Chang Z, Talukdar S, Shetty M, Mullany SA, Morgan M, Parmigiani G, Birrer MJ, Qin LX, Riester M, Starr TK, Waldron L.

    Cancer Res. 2020

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  • Multiomic Integration of Public Oncology Databases in Bioconductor

    Authors: Ramos M, Geistlinger L, Oh S, Schiffer L, Azhar R, Kodali H, de Bruijn I, Gao J, Carey VJ, Morgan M, Waldron L. JCO.

    Clin Cancer Inform. 2020

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

    Authors: Oh S, Geistlinger L, Ramos M, Morgan M, Waldron L, Riester M. JCO.

    Clin Cancer Inform. 2020

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  • Orchestrating single-cell analysis with Bioconductor

    Authors: Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC.

    Nat Methods. 2020

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  • CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.

    Authors: da Silva V, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho L, Zimmer R, Waldron L, Geistlinger L.

    Bioinformatics. 2020

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

    Authors: Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE, Waldron L.

    Ann Epidemiol. 2019

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  • Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma

    Authors: Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L.

    Clin Cancer Res. 2018

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

    Authors: Geistlinger L, da Silva VH, Cesar ASM, Tizioto PC, Waldron L, Zimmer R, Regitano LCA, Coutinho LL.

    Sci Rep. 2018

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

    Authors: Geistlinger L, Csaba G, Zimmer R.

    BMC Bioinformatics. 2016

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

    Authors: Geistlinger L, Csaba G, Dirmeier S, Küffner R, Zimmer R.

    Nucleic Acids Res. 2013

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

    Authors: Geistlinger L, Csaba G, Küffner R, Mulder N, Zimmer R.

    Bioinformatics. 2011

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  • Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum

    Authors: Gieger C, Geistlinger L, Altmaier E, Hrabé de Angelis M, Kronenberg F, Meitinger T, Mewes HW, Wichmann HE, Weinberger KM, Adamski J, Illig T, Suhre K.

    PLoS Genet. 2008

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