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.

  • 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. November 27, 2021

    View full abstract on Pubmed

  • 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 Feb;27

    View full abstract on Pubmed

  • 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 Jan 18;22

    View full abstract on Pubmed

  • 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 Oct 15

    View full abstract on Pubmed