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Items: 20

1.

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

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

Bioinformatics. 2019 Aug 8. pii: btz632. doi: 10.1093/bioinformatics/btz632. [Epub ahead of print]

PMID:
31392308
2.

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

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 Jun;34:18-25.e3. doi: 10.1016/j.annepidem.2019.03.005. Epub 2019 Mar 28.

PMID:
31076212
3.

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

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.

Front Genet. 2019 Mar 13;10:210. doi: 10.3389/fgene.2019.00210. eCollection 2019.

4.

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

Waldron L, Schiffer L, Azhar R, Ramos M, Geistlinger L, Segata N.

Am J Epidemiol. 2019 Jun 1;188(6):1031-1032. doi: 10.1093/aje/kwz008. No abstract available.

PMID:
30689687
5.

HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.

Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L.

Am J Epidemiol. 2019 Jun 1;188(6):1023-1026. doi: 10.1093/aje/kwz006.

PMID:
30649166
6.

Orchestrating a community-developed computational workshop and accompanying training materials.

Davis S, Ramos M, Shepherd L, Turaga N, Geistlinger L, Morgan MT, Haibe-Kains B, Waldron L.

F1000Res. 2018 Oct 17;7:1656. doi: 10.12688/f1000research.16516.1. eCollection 2018.

7.

A comprehensive manually-curated compendium of bovine transcription factors.

de Souza MM, Zerlotini A, Geistlinger L, Tizioto PC, Taylor JF, Rocha MIP, Diniz WJS, Coutinho LL, Regitano LCA.

Sci Rep. 2018 Sep 13;8(1):13747. doi: 10.1038/s41598-018-32146-2.

8.

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

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 Oct 15;24(20):5037-5047. doi: 10.1158/1078-0432.CCR-18-0784. Epub 2018 Jul 3.

9.

Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits.

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.

BMC Genomics. 2018 Jun 27;19(1):499. doi: 10.1186/s12864-018-4871-y.

10.

Micropatterning as a tool to identify regulatory triggers and kinetics of actin-mediated endothelial mechanosensing.

Gegenfurtner FA, Jahn B, Wagner H, Ziegenhain C, Enard W, Geistlinger L, Rädler JO, Vollmar AM, Zahler S.

J Cell Sci. 2018 May 29;131(10). pii: jcs212886. doi: 10.1242/jcs.212886.

11.

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

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

Sci Rep. 2018 Jan 23;8(1):1399. doi: 10.1038/s41598-018-19782-4.

12.

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

Silva VH, Regitano LC, Geistlinger L, Pértille F, Giachetto PF, Brassaloti RA, Morosini NS, Zimmer R, Coutinho LL.

PLoS One. 2016 Jun 27;11(6):e0157711. doi: 10.1371/journal.pone.0157711. eCollection 2016.

13.

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

Geistlinger L, Csaba G, Zimmer R.

BMC Bioinformatics. 2016 Jan 20;17:45. doi: 10.1186/s12859-016-0884-1.

14.

Addressing false discoveries in network inference.

Petri T, Altmann S, Geistlinger L, Zimmer R, Küffner R.

Bioinformatics. 2015 Sep 1;31(17):2836-43. doi: 10.1093/bioinformatics/btv215. Epub 2015 Apr 24.

PMID:
25910697
15.

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

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

Nucleic Acids Res. 2013 Oct;41(18):8452-63. doi: 10.1093/nar/gkt631. Epub 2013 Jul 19.

16.

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

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.

BMC Biotechnol. 2013 May 20;13:43. doi: 10.1186/1472-6750-13-43.

17.

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

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

Bioinformatics. 2011 Jul 1;27(13):i366-73. doi: 10.1093/bioinformatics/btr228.

18.

Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A.

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.

PLoS Genet. 2010 Nov 18;6(11):e1001213. doi: 10.1371/journal.pgen.1001213.

19.

Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes.

Wang Z, Ding G, Geistlinger L, Li H, Liu L, Zeng R, Tateno Y, Li Y.

Mol Biol Evol. 2011 Mar;28(3):1131-40. doi: 10.1093/molbev/msq268. Epub 2010 Oct 18.

PMID:
20956806
20.

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

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 Nov;4(11):e1000282. doi: 10.1371/journal.pgen.1000282. Epub 2008 Nov 28.

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