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Items: 1 to 20 of 233

1.

gtrellis: an R/Bioconductor package for making genome-level Trellis graphics.

Gu Z, Eils R, Schlesner M.

BMC Bioinformatics. 2016 Apr 18;17:169. doi: 10.1186/s12859-016-1051-4.

2.

Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children.

Bauer T, Trump S, Ishaque N, Thürmann L, Gu L, Bauer M, Bieg M, Gu Z, Weichenhan D, Mallm JP, Röder S, Herberth G, Takada E, Mücke O, Winter M, Junge KM, Grützmann K, Rolle-Kampczyk U, Wang Q, Lawerenz C, Borte M, Polte T, Schlesner M, Schanne M, Wiemann S, Geörg C, Stunnenberg HG, Plass C, Rippe K, Mizuguchi J, Herrmann C, Eils R, Lehmann I.

Mol Syst Biol. 2016 Mar 24;12(3):861. doi: 10.15252/msb.20156520.

3.

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes.

Johann PD, Erkek S, Zapatka M, Kerl K, Buchhalter I, Hovestadt V, Jones DT, Sturm D, Hermann C, Segura Wang M, Korshunov A, Rhyzova M, Gröbner S, Brabetz S, Chavez L, Bens S, Gröschel S, Kratochwil F, Wittmann A, Sieber L, Geörg C, Wolf S, Beck K, Oyen F, Capper D, van Sluis P, Volckmann R, Koster J, Versteeg R, von Deimling A, Milde T, Witt O, Kulozik AE, Ebinger M, Shalaby T, Grotzer M, Sumerauer D, Zamecnik J, Mora J, Jabado N, Taylor MD, Huang A, Aronica E, Bertoni A, Radlwimmer B, Pietsch T, Schüller U, Schneppenheim R, Northcott PA, Korbel JO, Siebert R, Frühwald MC, Lichter P, Eils R, Gajjar A, Hasselblatt M, Pfister SM, Kool M.

Cancer Cell. 2016 Mar 14;29(3):379-93. doi: 10.1016/j.ccell.2016.02.001. Epub 2016 Feb 25.

PMID:
26923874
4.

New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs.

Sturm D, Orr BA, Toprak UH, Hovestadt V, Jones DT, Capper D, Sill M, Buchhalter I, Northcott PA, Leis I, Ryzhova M, Koelsche C, Pfaff E, Allen SJ, Balasubramanian G, Worst BC, Pajtler KW, Brabetz S, Johann PD, Sahm F, Reimand J, Mackay A, Carvalho DM, Remke M, Phillips JJ, Perry A, Cowdrey C, Drissi R, Fouladi M, Giangaspero F, Łastowska M, Grajkowska W, Scheurlen W, Pietsch T, Hagel C, Gojo J, Lötsch D, Berger W, Slavc I, Haberler C, Jouvet A, Holm S, Hofer S, Prinz M, Keohane C, Fried I, Mawrin C, Scheie D, Mobley BC, Schniederjan MJ, Santi M, Buccoliero AM, Dahiya S, Kramm CM, von Bueren AO, von Hoff K, Rutkowski S, Herold-Mende C, Frühwald MC, Milde T, Hasselblatt M, Wesseling P, Rößler J, Schüller U, Ebinger M, Schittenhelm J, Frank S, Grobholz R, Vajtai I, Hans V, Schneppenheim R, Zitterbart K, Collins VP, Aronica E, Varlet P, Puget S, Dufour C, Grill J, Figarella-Branger D, Wolter M, Schuhmann MU, Shalaby T, Grotzer M, van Meter T, Monoranu CM, Felsberg J, Reifenberger G, Snuderl M, Forrester LA, Koster J, Versteeg R, Volckmann R, van Sluis P, Wolf S, Mikkelsen T, Gajjar A, Aldape K, Moore AS, Taylor MD, Jones C, Jabado N, Karajannis MA, Eils R, Schlesner M, Lichter P, von Deimling A, Pfister SM, Ellison DW, Korshunov A, Kool M.

Cell. 2016 Feb 25;164(5):1060-72. doi: 10.1016/j.cell.2016.01.015.

PMID:
26919435
5.

Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast.

Poos AM, Maicher A, Dieckmann AK, Oswald M, Eils R, Kupiec M, Luke B, König R.

Nucleic Acids Res. 2016 Feb 22. pii: gkw111. [Epub ahead of print]

6.

Death receptor-based enrichment of Cas9-expressing cells.

Liesche C, Venkatraman L, Aschenbrenner S, Grosse S, Grimm D, Eils R, Beaudouin J.

BMC Biotechnol. 2016 Feb 16;16:17. doi: 10.1186/s12896-016-0250-4.

7.

CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma.

Noll EM, Eisen C, Stenzinger A, Espinet E, Muckenhuber A, Klein C, Vogel V, Klaus B, Nadler W, Rösli C, Lutz C, Kulke M, Engelhardt J, Zickgraf FM, Espinosa O, Schlesner M, Jiang X, Kopp-Schneider A, Neuhaus P, Bahra M, Sinn BV, Eils R, Giese NA, Hackert T, Strobel O, Werner J, Büchler MW, Weichert W, Trumpp A, Sprick MR.

Nat Med. 2016 Mar;22(3):278-87. doi: 10.1038/nm.4038. Epub 2016 Feb 8.

PMID:
26855150
8.

Optogenetic control of nuclear protein export.

Niopek D, Wehler P, Roensch J, Eils R, Di Ventura B.

Nat Commun. 2016 Feb 8;7:10624. doi: 10.1038/ncomms10624.

9.

Active medulloblastoma enhancers reveal subgroup-specific cellular origins.

Lin CY, Erkek S, Tong Y, Yin L, Federation AJ, Zapatka M, Haldipur P, Kawauchi D, Risch T, Warnatz HJ, Worst BC, Ju B, Orr BA, Zeid R, Polaski DR, Segura-Wang M, Waszak SM, Jones DT, Kool M, Hovestadt V, Buchhalter I, Sieber L, Johann P, Chavez L, Gröschel S, Ryzhova M, Korshunov A, Chen W, Chizhikov VV, Millen KJ, Amstislavskiy V, Lehrach H, Yaspo ML, Eils R, Lichter P, Korbel JO, Pfister SM, Bradner JE, Northcott PA.

Nature. 2016 Feb 4;530(7588):57-62. doi: 10.1038/nature16546. Epub 2016 Jan 27.

PMID:
26814967
10.

A comprehensive comparison of tools for differential ChIP-seq analysis.

Steinhauser S, Kurzawa N, Eils R, Herrmann C.

Brief Bioinform. 2016 Jan 13. pii: bbv110. [Epub ahead of print]

PMID:
26764273
12.

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG.

Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001.

13.

Automated Analysis of Single-Molecule Photobleaching Data by Statistical Modeling of Spot Populations.

Liesche C, Grussmayer KS, Ludwig M, Wörz S, Rohr K, Herten DP, Beaudouin J, Eils R.

Biophys J. 2015 Dec 1;109(11):2352-62. doi: 10.1016/j.bpj.2015.10.035.

PMID:
26636946
14.

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.

Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL.

BMC Genomics. 2015 Nov 21;16:982. doi: 10.1186/s12864-015-2137-5.

15.

Combinatorial treatment of CD95L and gemcitabine in pancreatic cancer cells induces apoptotic and RIP1-mediated necroptotic cell death network.

Pietkiewicz S, Eils R, Krammer PH, Giese N, Lavrik IN.

Exp Cell Res. 2015 Nov 15;339(1):1-9. doi: 10.1016/j.yexcr.2015.10.005. Epub 2015 Oct 8.

PMID:
26453936
16.

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.

Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Hummel M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenze D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nagel I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG; ICGC MMML-Seq project; BLUEPRINT project, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B.

Nat Genet. 2015 Nov;47(11):1316-25. doi: 10.1038/ng.3413. Epub 2015 Oct 5.

PMID:
26437030
17.

Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation.

Waldhauer MC, Schmitz SN, Ahlmann-Eltze C, Gleixner JG, Schmelas CC, Huhn AG, Bunne C, Büscher M, Horn M, Klughammer N, Kreft J, Schäfer E, Bayer PA, Krämer SG, Neugebauer J, Wehler P, Mayer MP, Eils R, Di Ventura B.

Mol Biosyst. 2015 Dec;11(12):3231-43. doi: 10.1039/c5mb00341e.

PMID:
26434634
18.

One, two or three? Probing the stoichiometry of membrane proteins by single-molecule localization microscopy.

Fricke F, Beaudouin J, Eils R, Heilemann M.

Sci Rep. 2015 Sep 11;5:14072. doi: 10.1038/srep14072.

19.

Increased vitamin D levels at birth and in early infancy increase offspring allergy risk-evidence for involvement of epigenetic mechanisms.

Junge KM, Bauer T, Geissler S, Hirche F, Thürmann L, Bauer M, Trump S, Bieg M, Weichenhan D, Gu L, Mallm JP, Ishaque N, Mücke O, Röder S, Herberth G, Diez U, Borte M, Rippe K, Plass C, Hermann C, Stangl GI, Eils R, Lehmann I.

J Allergy Clin Immunol. 2016 Feb;137(2):610-3. doi: 10.1016/j.jaci.2015.06.040. Epub 2015 Aug 15. No abstract available.

PMID:
26282283
20.

So rare we need to hunt for them: reframing the ethical debate on incidental findings.

Schuol S, Schickhardt C, Wiemann S, Bartram CR, Tanner K, Eils R, Meder B, Richter D, Glimm H, von Kalle C, Winkler EC.

Genome Med. 2015 Jul 30;7(1):83. doi: 10.1186/s13073-015-0198-3. eCollection 2015.

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