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Items: 49

1.

Inhibition of oxidative stress in cholinergic projection neurons fully rescues aging-associated olfactory circuit degeneration in Drosophila.

Hussain A, Pooryasin A, Zhang M, Loschek LF, La Fortezza M, Friedrich AB, Blais CM, Üçpunar HK, Yépez VA, Lehmann M, Gompel N, Gagneur J, Sigrist SJ, Grunwald Kadow IC.

Elife. 2018 Jan 18;7. pii: e32018. doi: 10.7554/eLife.32018.

2.

Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.

Avsec Ž, Barekatain M, Cheng J, Gagneur J.

Bioinformatics. 2018 Apr 15;34(8):1261-1269. doi: 10.1093/bioinformatics/btx727.

PMID:
29155928
3.

Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast.

Cheng J, Maier KC, Avsec Ž, Rus P, Gagneur J.

RNA. 2017 Nov;23(11):1648-1659. doi: 10.1261/rna.062224.117. Epub 2017 Aug 11.

4.

Caenorhabditis elegans CES-1 Snail Represses pig-1 MELK Expression To Control Asymmetric Cell Division.

Wei H, Yan B, Gagneur J, Conradt B.

Genetics. 2017 Aug;206(4):2069-2084. doi: 10.1534/genetics.117.202754. Epub 2017 Jun 26.

5.

Genetic diagnosis of Mendelian disorders via RNA sequencing.

Kremer LS, Bader DM, Mertes C, Kopajtich R, Pichler G, Iuso A, Haack TB, Graf E, Schwarzmayr T, Terrile C, Koňaříková E, Repp B, Kastenmüller G, Adamski J, Lichtner P, Leonhardt C, Funalot B, Donati A, Tiranti V, Lombes A, Jardel C, Gläser D, Taylor RW, Ghezzi D, Mayr JA, Rötig A, Freisinger P, Distelmaier F, Strom TM, Meitinger T, Gagneur J, Prokisch H.

Nat Commun. 2017 Jun 12;8:15824. doi: 10.1038/ncomms15824.

6.

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.

Stricker G, Engelhardt A, Schulz D, Schmid M, Tresch A, Gagneur J.

Bioinformatics. 2017 Aug 1;33(15):2258-2265. doi: 10.1093/bioinformatics/btx150.

PMID:
28369277
7.

Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes.

Witzel M, Petersheim D, Fan Y, Bahrami E, Racek T, Rohlfs M, Puchałka J, Mertes C, Gagneur J, Ziegenhain C, Enard W, Stray-Pedersen A, Arkwright PD, Abboud MR, Pazhakh V, Lieschke GJ, Krawitz PM, Dahlhoff M, Schneider MR, Wolf E, Horny HP, Schmidt H, Schäffer AA, Klein C.

Nat Genet. 2017 May;49(5):742-752. doi: 10.1038/ng.3833. Epub 2017 Apr 3.

8.

TT-seq captures enhancer landscapes immediately after T-cell stimulation.

Michel M, Demel C, Zacher B, Schwalb B, Krebs S, Blum H, Gagneur J, Cramer P.

Mol Syst Biol. 2017 Mar 7;13(3):920. doi: 10.15252/msb.20167507.

9.

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN.

Zacher B, Michel M, Schwalb B, Cramer P, Tresch A, Gagneur J.

PLoS One. 2017 Jan 5;12(1):e0169249. doi: 10.1371/journal.pone.0169249. eCollection 2017.

10.

Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Early-Onset Severe Encephalopathy.

Ait-El-Mkadem S, Dayem-Quere M, Gusic M, Chaussenot A, Bannwarth S, François B, Genin EC, Fragaki K, Volker-Touw CLM, Vasnier C, Serre V, van Gassen KLI, Lespinasse F, Richter S, Eisenhofer G, Rouzier C, Mochel F, De Saint-Martin A, Abi Warde MT, de Sain-van der Velde MGM, Jans JJM, Amiel J, Avsec Z, Mertes C, Haack TB, Strom T, Meitinger T, Bonnen PE, Taylor RW, Gagneur J, van Hasselt PM, Rötig A, Delahodde A, Prokisch H, Fuchs SA, Paquis-Flucklinger V.

Am J Hum Genet. 2017 Jan 5;100(1):151-159. doi: 10.1016/j.ajhg.2016.11.014. Epub 2016 Dec 15.

11.

Measures of RNA metabolism rates: Toward a definition at the level of single bonds.

Wachutka L, Gagneur J.

Transcription. 2017 Mar 15;8(2):75-80. doi: 10.1080/21541264.2016.1257972. Epub 2016 Nov 14.

12.

Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant.

Gupta S, Radhakrishnan A, Nitin R, Raharja-Liu P, Lin G, Steinmetz LM, Gagneur J, Sinha H.

G3 (Bethesda). 2016 Aug 9;6(8):2255-63. doi: 10.1534/g3.116.029900.

13.

TT-seq maps the human transient transcriptome.

Schwalb B, Michel M, Zacher B, Frühauf K, Demel C, Tresch A, Gagneur J, Cramer P.

Science. 2016 Jun 3;352(6290):1225-8. doi: 10.1126/science.aad9841.

14.

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome.

Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J.

Mol Syst Biol. 2016 Feb 16;12(2):857. doi: 10.15252/msb.20156526.

15.

Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model.

Glas J, Dümcke S, Zacher B, Poron D, Gagneur J, Tresch A.

Nucleic Acids Res. 2016 Mar 18;44(5):e44. doi: 10.1093/nar/gkv1184. Epub 2015 Nov 17.

16.

Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy.

Haack TB, Staufner C, Köpke MG, Straub BK, Kölker S, Thiel C, Freisinger P, Baric I, McKiernan PJ, Dikow N, Harting I, Beisse F, Burgard P, Kotzaeridou U, Kühr J, Himbert U, Taylor RW, Distelmaier F, Vockley J, Ghaloul-Gonzalez L, Zschocke J, Kremer LS, Graf E, Schwarzmayr T, Bader DM, Gagneur J, Wieland T, Terrile C, Strom TM, Meitinger T, Hoffmann GF, Prokisch H.

Am J Hum Genet. 2015 Jul 2;97(1):163-9. doi: 10.1016/j.ajhg.2015.05.009. Epub 2015 Jun 11.

17.

Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype.

Gupta S, Radhakrishnan A, Raharja-Liu P, Lin G, Steinmetz LM, Gagneur J, Sinha H.

PLoS Genet. 2015 Jun 3;11(6):e1005195. doi: 10.1371/journal.pgen.1005195. eCollection 2015 Jun.

18.

Negative feedback buffers effects of regulatory variants.

Bader DM, Wilkening S, Lin G, Tekkedil MM, Dietrich K, Steinmetz LM, Gagneur J.

Mol Syst Biol. 2015 Jan 29;11(1):785. doi: 10.15252/msb.20145844.

19.

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A.

Mol Syst Biol. 2014 Dec 19;10:768. doi: 10.15252/msb.20145654.

20.

Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders.

Aiyar RS, Bohnert M, Duvezin-Caubet S, Voisset C, Gagneur J, Fritsch ES, Couplan E, von der Malsburg K, Funaya C, Soubigou F, Courtin F, Suresh S, Kucharczyk R, Evrard J, Antony C, St Onge RP, Blondel M, di Rago JP, van der Laan M, Steinmetz LM.

Nat Commun. 2014 Dec 18;5:5585. doi: 10.1038/ncomms6585.

21.

An improvement in IMRT QA results and beam matching in linacs using statistical process control.

Gagneur JD, Ezzell GA.

J Appl Clin Med Phys. 2014 Sep 8;15(5):4927. doi: 10.1120/jacmp.v15i5.4927.

22.

Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.

Bhatia A, Yadav A, Zhu C, Gagneur J, Radhakrishnan A, Steinmetz LM, Bhanot G, Sinha H.

G3 (Bethesda). 2014 Jan 28;4(5):769-77. doi: 10.1534/g3.113.009142.

23.

An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae.

Wilkening S, Lin G, Fritsch ES, Tekkedil MM, Anders S, Kuehn R, Nguyen M, Aiyar RS, Proctor M, Sakhanenko NA, Galas DJ, Gagneur J, Deutschbauer A, Steinmetz LM.

Genetics. 2014 Mar;196(3):853-65. doi: 10.1534/genetics.113.160291. Epub 2013 Dec 27.

24.

Transcriptome surveillance by selective termination of noncoding RNA synthesis.

Schulz D, Schwalb B, Kiesel A, Baejen C, Torkler P, Gagneur J, Soeding J, Cramer P.

Cell. 2013 Nov 21;155(5):1075-87. doi: 10.1016/j.cell.2013.10.024. Epub 2013 Nov 7.

25.

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.

Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM.

PLoS Genet. 2013;9(9):e1003803. doi: 10.1371/journal.pgen.1003803. Epub 2013 Sep 19.

26.

The genomic and transcriptomic landscape of a HeLa cell line.

Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM.

G3 (Bethesda). 2013 Aug 7;3(8):1213-24. doi: 10.1534/g3.113.005777.

27.

Genotyping 1000 yeast strains by next-generation sequencing.

Wilkening S, Tekkedil MM, Lin G, Fritsch ES, Wei W, Gagneur J, Lazinski DW, Camilli A, Steinmetz LM.

BMC Genomics. 2013 Feb 9;14:90. doi: 10.1186/1471-2164-14-90.

28.

Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution.

Bietenhader M, Martos A, Tetaud E, Aiyar RS, Sellem CH, Kucharczyk R, Clauder-Münster S, Giraud MF, Godard F, Salin B, Sagot I, Gagneur J, Déquard-Chablat M, Contamine V, Hermann-Le Denmat S, Sainsard-Chanet A, Steinmetz LM, di Rago JP.

PLoS Genet. 2012;8(8):e1002876. doi: 10.1371/journal.pgen.1002876. Epub 2012 Aug 16.

29.

Selective phenotyping, entropy reduction, and the mastermind game.

Gagneur J, Elze MC, Tresch A.

BMC Bioinformatics. 2011 Oct 20;12:406. doi: 10.1186/1471-2105-12-406.

30.

A yeast-based assay identifies drugs active against human mitochondrial disorders.

Couplan E, Aiyar RS, Kucharczyk R, Kabala A, Ezkurdia N, Gagneur J, St Onge RP, Salin B, Soubigou F, Le Cann M, Steinmetz LM, di Rago JP, Blondel M.

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11989-94. doi: 10.1073/pnas.1101478108. Epub 2011 Jun 29.

31.

Model-based gene set analysis for Bioconductor.

Bauer S, Robinson PN, Gagneur J.

Bioinformatics. 2011 Jul 1;27(13):1882-3. doi: 10.1093/bioinformatics/btr296. Epub 2011 May 10.

32.

Antisense expression increases gene expression variability and locus interdependency.

Xu Z, Wei W, Gagneur J, Clauder-Münster S, Smolik M, Huber W, Steinmetz LM.

Mol Syst Biol. 2011 Feb 15;7:468. doi: 10.1038/msb.2011.1.

33.

GOing Bayesian: model-based gene set analysis of genome-scale data.

Bauer S, Gagneur J, Robinson PN.

Nucleic Acids Res. 2010 Jun;38(11):3523-32. doi: 10.1093/nar/gkq045. Epub 2010 Feb 19.

34.

Combinatorial binding predicts spatio-temporal cis-regulatory activity.

Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE.

Nature. 2009 Nov 5;462(7269):65-70. doi: 10.1038/nature08531.

PMID:
19890324
35.

Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae.

Blandin SA, Wang-Sattler R, Lamacchia M, Gagneur J, Lycett G, Ning Y, Levashina EA, Steinmetz LM.

Science. 2009 Oct 2;326(5949):147-50. doi: 10.1126/science.1175241.

36.

Genome-wide allele- and strand-specific expression profiling.

Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM.

Mol Syst Biol. 2009;5:274. doi: 10.1038/msb.2009.31. Epub 2009 Jun 16.

37.

Bidirectional promoters generate pervasive transcription in yeast.

Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM.

Nature. 2009 Feb 19;457(7232):1033-7. doi: 10.1038/nature07728. Epub 2009 Jan 25.

38.

Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila.

Oktaba K, Gutiérrez L, Gagneur J, Girardot C, Sengupta AK, Furlong EE, Müller J.

Dev Cell. 2008 Dec;15(6):877-89. doi: 10.1016/j.devcel.2008.10.005. Epub 2008 Nov 6.

39.

Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

Aiyar RS, Gagneur J, Steinmetz LM.

Methods. 2008 Dec;46(4):248-55. doi: 10.1016/j.ymeth.2008.10.002. Epub 2008 Oct 16.

40.

4DXpress: a database for cross-species expression pattern comparisons.

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53. Epub 2007 Oct 4.

41.

Assessing systems properties of yeast mitochondria through an interaction map of the organelle.

Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM.

PLoS Genet. 2006 Oct 20;2(10):e170.

42.

Algorithmic approaches for computing elementary modes in large biochemical reaction networks.

Klamt S, Gagneur J, von Kamp A.

Syst Biol (Stevenage). 2005 Dec;152(4):249-55.

PMID:
16986267
43.

Capturing cellular machines by systematic screens of protein complexes.

Gagneur J, David L, Steinmetz LM.

Trends Microbiol. 2006 Aug;14(8):336-9. Epub 2006 Jun 16. Review.

PMID:
16782340
44.

Impact of the longitudinal and seasonal changes of the water quality on the benthic macroinvertebrate assemblages of the Andorran streams.

Younes-Baraillé Y, Garcia XF, Gagneur J.

C R Biol. 2005 Oct-Nov;328(10-11):963-76. Epub 2005 Oct 28.

PMID:
16286086
45.

From molecular networks to qualitative cell behavior.

Gagneur J, Casari G.

FEBS Lett. 2005 Mar 21;579(8):1867-71. Review.

46.
47.

Modular decomposition of protein-protein interaction networks.

Gagneur J, Krause R, Bouwmeester T, Casari G.

Genome Biol. 2004;5(8):R57. Epub 2004 Jul 21.

48.

A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway.

Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, Hopf C, Huhse B, Mangano R, Michon AM, Schirle M, Schlegl J, Schwab M, Stein MA, Bauer A, Casari G, Drewes G, Gavin AC, Jackson DB, Joberty G, Neubauer G, Rick J, Kuster B, Superti-Furga G.

Nat Cell Biol. 2004 Feb;6(2):97-105. Epub 2004 Jan 25. Erratum in: Nat Cell Biol. 2004 May;6(5):465.

PMID:
14743216
49.

Hierarchical analysis of dependency in metabolic networks.

Gagneur J, Jackson DB, Casari G.

Bioinformatics. 2003 May 22;19(8):1027-34.

PMID:
12761067

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