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Ludwig Geistlinger, Ph.D.


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Geistlinger L, Vargas R, Lee T, Pan J, Huttlin EL, Gentleman R. BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions. Bioinformatics. 2023 03 01; 39(3). PMID: 36794911; PMCID: PMC9978581.
    Citations:    Fields:    Translation:HumansCells
  2. Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun. 2022 06 27; 13(1):3695. PMID: 35760813; PMCID: PMC9237024.
    Citations: 2     Fields:    Translation:HumansCells
  3. Mirzayi C, Renson A, 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. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021 11; 27(11):1885-1892. PMID: 34789871; PMCID: PMC9105086.
    Citations: 48     Fields:    Translation:Humans
  4. Geistlinger L, Csaba G, Santarelli M, Ramos M, Schiffer L, Turaga N, Law C, Davis S, Carey V, Morgan M, Zimmer R, Waldron L. Toward a gold standard for benchmarking gene set enrichment analysis. Brief Bioinform. 2021 01 18; 22(1):545-556. PMID: 32026945; PMCID: PMC7820859.
    Citations: 40     Fields:    Translation:HumansAnimals
  5. 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. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med. 2021 02; 27(2):321-332. PMID: 33432175; PMCID: PMC8353542.
    Citations: 163     Fields:    Translation:HumansAnimalsCellsPHPublic HealthCTClinical Trials
  6. Tomic A, Tomic I, Waldron L, Geistlinger L, Kuhn M, Spreng RL, Dahora LC, Seaton KE, Tomaras G, Hill J, Duggal NA, Pollock RD, Lazarus NR, Harridge SDR, Lord JM, Khatri P, Pollard AJ, Davis MM. SIMON: Open-Source Knowledge Discovery Platform. Patterns (N Y). 2021 Jan 08; 2(1):100178. PMID: 33511368; PMCID: PMC7815964.
    Citations: 3     
  7. Ramos M, Geistlinger L, Oh S, Schiffer L, Azhar R, Kodali H, de Bruijn I, Gao J, Carey VJ, Morgan M, Waldron L. Multiomic Integration of Public Oncology Databases in Bioconductor. JCO Clin Cancer Inform. 2020 10; 4:958-971. PMID: 33119407.
    Citations: 9     Fields:    Translation:Humans
  8. 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. Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res. 2020 10 15; 80(20):4335-4345. PMID: 32747365.
    Citations: 24     Fields:    Translation:Humans
  9. Oh S, Geistlinger L, Ramos M, Morgan M, Waldron L, Riester M. Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data. JCO Clin Cancer Inform. 2020 04; 4:321-335. PMID: 32282230.
    Citations: 9     Fields:    Translation:Humans
  10. 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. Publisher Correction: Orchestrating single-cell analysis with Bioconductor. Nat Methods. 2020 Feb; 17(2):242. PMID: 31827272.
    Citations: 1     Fields:    
  11. da Silva V, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho L, Zimmer R, Waldron L, Geistlinger L. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinformatics. 2020 02 01; 36(3):972-973. PMID: 31392308; PMCID: PMC9887538.
    Citations: 4     Fields:    
  12. 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. Orchestrating single-cell analysis with Bioconductor. Nat Methods. 2020 02; 17(2):137-145. PMID: 31792435; PMCID: PMC7358058.
    Citations: 138     Fields:    
  13. Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L. HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Am J Epidemiol. 2019 06 01; 188(6):1023-1026. PMID: 30649166; PMCID: PMC6545282.
    Citations: 16     Fields:    Translation:Humans
  14. Waldron L, Schiffer L, Azhar R, Ramos M, Geistlinger L, Segata N. Waldron et al. Reply to "Commentary on the HMP16SData Bioconductor Package". Am J Epidemiol. 2019 06 01; 188(6):1031-1032. PMID: 30689687; PMCID: PMC6545274.
    Citations:    Fields:    Translation:Humans
  15. Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE, Waldron L. Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study. Ann Epidemiol. 2019 06; 34:18-25.e3. PMID: 31076212; PMCID: PMC6548637.
    Citations: 14     Fields:    Translation:HumansPHPublic Health
  16. Diniz WJS, Mazzoni G, Coutinho LL, Banerjee P, Geistlinger L, Cesar ASM, Bertolini F, Afonso J, de Oliveira PSN, Tizioto PC, Kadarmideen HN, Regitano LCA. Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle. Front Genet. 2019; 10:210. PMID: 30930938; PMCID: PMC6424907.
    Citations: 11     
  17. Davis S, Ramos M, Shepherd L, Turaga N, Geistlinger L, Morgan MT, Haibe-Kains B, Waldron L. Orchestrating a community-developed computational workshop and accompanying training materials. F1000Res. 2018; 7:1656. PMID: 30473781; PMCID: PMC6234736.
    Citations: 1     Fields:    
  18. de Souza MM, Zerlotini A, Geistlinger L, Tizioto PC, Taylor JF, Rocha MIP, Diniz WJS, Coutinho LL, Regitano LCA. A comprehensive manually-curated compendium of bovine transcription factors. Sci Rep. 2018 09 13; 8(1):13747. PMID: 30213987.
    Citations: 11     Fields:    Translation:HumansAnimals
  19. Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L. Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin Cancer Res. 2018 10 15; 24(20):5037-5047. PMID: 30084834; PMCID: PMC6207081.
    Citations: 38     Fields:    Translation:Humans
  20. Cesar ASM, Regitano LCA, Reecy JM, Poleti MD, Oliveira PSN, de Oliveira GB, Moreira GCM, Mudadu MA, Tizioto PC, Koltes JE, Fritz-Waters E, Kramer L, Garrick D, Beiki H, Geistlinger L, Mourão GB, Zerlotini A, Coutinho LL. Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. BMC Genomics. 2018 Jun 27; 19(1):499. PMID: 29945546.
    Citations: 19     Fields:    Translation:AnimalsCells
  21. Gegenfurtner FA, Jahn B, Wagner H, Ziegenhain C, Enard W, Geistlinger L, Rädler JO, Vollmar AM, Zahler S. Micropatterning as a tool to identify regulatory triggers and kinetics of actin-mediated endothelial mechanosensing. J Cell Sci. 2018 05 29; 131(10). PMID: 29724912.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  22. Geistlinger L, da Silva VH, Cesar ASM, Tizioto PC, Waldron L, Zimmer R, Regitano LCA, Coutinho LL. Widespread modulation of gene expression by copy number variation in skeletal muscle. Sci Rep. 2018 01 23; 8(1):1399. PMID: 29362391; PMCID: PMC5780461.
    Citations: 10     Fields:    Translation:Animals
  23. Silva VH, Regitano LC, Geistlinger L, Pértille F, Giachetto PF, Brassaloti RA, Morosini NS, Zimmer R, Coutinho LL. Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLoS One. 2016; 11(6):e0157711. PMID: 27348523.
    Citations: 20     Fields:    Translation:Animals
  24. Geistlinger L, Csaba G, Zimmer R. Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinformatics. 2016 Jan 20; 17:45. PMID: 26791995.
    Citations: 27     Fields:    
  25. Petri T, Altmann S, Geistlinger L, Zimmer R, Küffner R. Addressing false discoveries in network inference. Bioinformatics. 2015 Sep 01; 31(17):2836-43. PMID: 25910697.
    Citations: 9     Fields:    Translation:Cells
  26. Geistlinger L, Csaba G, Dirmeier S, Küffner R, Zimmer R. A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Res. 2013 Oct; 41(18):8452-63. PMID: 23873954.
    Citations: 7     Fields:    Translation:AnimalsCells
  27. Kurome M, Geistlinger L, Kessler B, Zakhartchenko V, Klymiuk N, Wuensch A, Richter A, Baehr A, Kraehe K, Burkhardt K, Flisikowski K, Flisikowska T, Merkl C, Landmann M, Durkovic M, Tschukes A, Kraner S, Schindelhauer D, Petri T, Kind A, Nagashima H, Schnieke A, Zimmer R, Wolf E. Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set. BMC Biotechnol. 2013 May 20; 13:43. PMID: 23688045.
    Citations: 32     Fields:    Translation:Animals
  28. Geistlinger L, Csaba G, Küffner R, Mulder N, Zimmer R. From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics. 2011 Jul 01; 27(13):i366-73. PMID: 21685094.
    Citations: 29     Fields:    Translation:HumansCells
  29. Marzi C, Albrecht E, Hysi PG, Lagou V, Waldenberger M, Tönjes A, Prokopenko I, Heim K, Blackburn H, Ried JS, Kleber ME, Mangino M, Thorand B, Peters A, Hammond CJ, Grallert H, Boehm BO, Kovacs P, Geistlinger L, Prokisch H, Winkelmann BR, Spector TD, Wichmann HE, Stumvoll M, Soranzo N, März W, Koenig W, Illig T, Gieger C. Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A. PLoS Genet. 2010 Nov 18; 6(11):e1001213. PMID: 21124955.
    Citations: 14     Fields:    Translation:HumansCells
  30. Wang Z, Ding G, Geistlinger L, Li H, Liu L, Zeng R, Tateno Y, Li Y. Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. Mol Biol Evol. 2011 Mar; 28(3):1131-40. PMID: 20956806.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  31. 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. Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet. 2008 Nov; 4(11):e1000282. PMID: 19043545; PMCID: PMC2581785.
    Citations: 313     Fields:    Translation:Humans
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.