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Items: 1 to 50 of 77

1.

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.

Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J.

Cell. 2019 Sep 5;178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018.

PMID:
31491388
2.

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.

Shao W, Guo T, Toussaint NC, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser CD, Poyet C, Ljubicic J, Rupp N, Rüschoff JH, Zhong Q, Beyer A, Ji J, Collins BC, Liu Y, Rätsch G, Wild PJ, Aebersold R.

Nat Commun. 2019 Jun 7;10(1):2524. doi: 10.1038/s41467-019-10513-5.

3.

c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma.

Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Sun L, Yong-Gonzalez V, Viale A, Cross JR, Hendrickson RC, Rätsch G, Ouyang Z, Wendel HG.

J Exp Med. 2019 Jul 1;216(7):1509-1524. doi: 10.1084/jem.20181726. Epub 2019 May 29.

PMID:
31142587
4.

HBEGF+ macrophages in rheumatoid arthritis induce fibroblast invasiveness.

Kuo D, Ding J, Cohn IS, Zhang F, Wei K, Rao DA, Rozo C, Sokhi UK, Shanaj S, Oliver DJ, Echeverria AP, DiCarlo EF, Brenner MB, Bykerk VP, Goodman SM, Raychaudhuri S, Rätsch G, Ivashkiv LB, Donlin LT.

Sci Transl Med. 2019 May 8;11(491). pii: eaau8587. doi: 10.1126/scitranslmed.aau8587.

5.

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2.

Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, Goldgar D, Goldman MJ, Goodhand P, Harrison S, Haussler D, Kato K, Knoppers B, Markello C, Nussbaum R, Offit K, Plon SE, Rashbass J, Rehm HL, Robson M, Rubinstein WS, Stoppa-Lyonnet D, Tavtigian S, Thorogood A, Zhang C, Zimmermann M; BRCA Challenge Authors, Burn J, Chanock S, Rätsch G, Spurdle AB.

PLoS Genet. 2018 Dec 26;14(12):e1007752. doi: 10.1371/journal.pgen.1007752. eCollection 2018 Dec.

6.

EIF1AX and RAS Mutations Cooperate to Drive Thyroid Tumorigenesis through ATF4 and c-MYC.

Krishnamoorthy GP, Davidson NR, Leach SD, Zhao Z, Lowe SW, Lee G, Landa I, Nagarajah J, Saqcena M, Singh K, Wendel HG, Dogan S, Tamarapu PP, Blenis J, Ghossein RA, Knauf JA, Rätsch G, Fagin JA.

Cancer Discov. 2019 Feb;9(2):264-281. doi: 10.1158/2159-8290.CD-18-0606. Epub 2018 Oct 10.

PMID:
30305285
7.

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C; Cancer Genome Atlas Research Network, Rätsch G.

Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2.

8.

Registered access: authorizing data access.

Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P.

Eur J Hum Genet. 2018 Dec;26(12):1721-1731. doi: 10.1038/s41431-018-0219-y. Epub 2018 Aug 2.

9.

Dynamic compression schemes for graph coloring.

Mustafa H, Schilken I, Karasikov M, Eickhoff C, Rätsch G, Kahles A.

Bioinformatics. 2019 Feb 1;35(3):407-414. doi: 10.1093/bioinformatics/bty632.

10.

Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes.

Loupasakis K, Kuo D, Sokhi UK, Sohn C, Syracuse B, Giannopoulou EG, Park SH, Kang H, Rätsch G, Ivashkiv LB, Kalliolias GD.

PLoS One. 2017 Jul 14;12(7):e0179762. doi: 10.1371/journal.pone.0179762. eCollection 2017.

11.

Prediction of potent shRNAs with a sequential classification algorithm.

Pelossof R, Fairchild L, Huang CH, Widmer C, Sreedharan VT, Sinha N, Lai DY, Guan Y, Premsrirut PK, Tschaharganeh DF, Hoffmann T, Thapar V, Xiang Q, Garippa RJ, Rätsch G, Zuber J, Lowe SW, Leslie CS, Fellmann C.

Nat Biotechnol. 2017 Apr;35(4):350-353. doi: 10.1038/nbt.3807. Epub 2017 Mar 6.

12.

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.

Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R.

Genetics. 2017 Apr;205(4):1425-1441. doi: 10.1534/genetics.116.192823. Epub 2017 Feb 7.

13.

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.

Hartmann L, Drewe-Boß P, Wießner T, Wagner G, Geue S, Lee HC, Obermüller DM, Kahles A, Behr J, Sinz FH, Rätsch G, Wachter A.

Plant Cell. 2016 Nov;28(11):2715-2734. Epub 2016 Nov 1.

14.

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.

Zhong Y, Karaletsos T, Drewe P, Sreedharan VT, Kuo D, Singh K, Wendel HG, Rätsch G.

Bioinformatics. 2017 Jan 1;33(1):139-141. doi: 10.1093/bioinformatics/btw585. Epub 2016 Sep 14.

15.

Efficient privacy-preserving string search and an application in genomics.

Shimizu K, Nuida K, Rätsch G.

Bioinformatics. 2016 Jun 1;32(11):1652-61. doi: 10.1093/bioinformatics/btw050. Epub 2016 Mar 2.

16.

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.

Kahles A, Ong CS, Zhong Y, Rätsch G.

Bioinformatics. 2016 Jun 15;32(12):1840-7. doi: 10.1093/bioinformatics/btw076. Epub 2016 Feb 11.

17.

SVM2Motif--Reconstructing Overlapping DNA Sequence Motifs by Mimicking an SVM Predictor.

Vidovic MM, Görnitz N, Müller KR, Rätsch G, Kloft M.

PLoS One. 2015 Dec 21;10(12):e0144782. doi: 10.1371/journal.pone.0144782. eCollection 2015.

18.

MMR: a tool for read multi-mapper resolution.

Kahles A, Behr J, Rätsch G.

Bioinformatics. 2016 Mar 1;32(5):770-2. doi: 10.1093/bioinformatics/btv624. Epub 2015 Oct 30.

19.

Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation.

Su X, Yu Y, Zhong Y, Giannopoulou EG, Hu X, Liu H, Cross JR, Rätsch G, Rice CM, Ivashkiv LB.

Nat Immunol. 2015 Aug;16(8):838-849. doi: 10.1038/ni.3205. Epub 2015 Jun 29.

20.

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M.

Elife. 2015 May 5;4:e05255. doi: 10.7554/eLife.05255.

21.

Graph-regularized 3D shape reconstruction from highly anisotropic and noisy images.

Widmer C, Heinrich S, Drewe P, Lou X, Umrania S, Rätsch G.

Signal Image Video Process. 2014 Dec 1;8(1 Suppl):41-48.

22.

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G.

Pac Symp Biocomput. 2015:44-55.

23.

Genome-wide analysis of alternative splicing in Volvox carteri.

Kianianmomeni A, Ong CS, Rätsch G, Hallmann A.

BMC Genomics. 2014 Dec 16;15:1117. doi: 10.1186/1471-2164-15-1117.

24.

Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis.

Chae E, Bomblies K, Kim ST, Karelina D, Zaidem M, Ossowski S, Martín-Pizarro C, Laitinen RA, Rowan BA, Tenenboim H, Lechner S, Demar M, Habring-Müller A, Lanz C, Rätsch G, Weigel D.

Cell. 2014 Dec 4;159(6):1341-51. doi: 10.1016/j.cell.2014.10.049. Epub 2014 Nov 20.

25.

Determination and inference of eukaryotic transcription factor sequence specificity.

Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR.

Cell. 2014 Sep 11;158(6):1431-1443. doi: 10.1016/j.cell.2014.08.009.

26.

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer.

Wolfe AL, Singh K, Zhong Y, Drewe P, Rajasekhar VK, Sanghvi VR, Mavrakis KJ, Jiang M, Roderick JE, Van der Meulen J, Schatz JH, Rodrigo CM, Zhao C, Rondou P, de Stanchina E, Teruya-Feldstein J, Kelliher MA, Speleman F, Porco JA Jr, Pelletier J, Rätsch G, Wendel HG.

Nature. 2014 Sep 4;513(7516):65-70. doi: 10.1038/nature13485. Epub 2014 Jul 27.

27.

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G.

Bioinformatics. 2014 May 1;30(9):1300-1. doi: 10.1093/bioinformatics/btt731. Epub 2014 Jan 11.

28.

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota.

Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB.

PLoS Comput Biol. 2013;9(12):e1003388. doi: 10.1371/journal.pcbi.1003388. Epub 2013 Dec 12.

29.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium.

Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.

30.

Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome.

Drechsel G, Kahles A, Kesarwani AK, Stauffer E, Behr J, Drewe P, Rätsch G, Wachter A.

Plant Cell. 2013 Oct;25(10):3726-42. doi: 10.1105/tpc.113.115485. Epub 2013 Oct 25.

31.

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G.

Bioinformatics. 2013 Oct 15;29(20):2529-38. doi: 10.1093/bioinformatics/btt442. Epub 2013 Aug 25.

32.

Accurate detection of differential RNA processing.

Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G.

Nucleic Acids Res. 2013 May 1;41(10):5189-98. doi: 10.1093/nar/gkt211. Epub 2013 Apr 12.

33.

Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes.

Rühl C, Stauffer E, Kahles A, Wagner G, Drechsel G, Rätsch G, Wachter A.

Plant Cell. 2012 Nov;24(11):4360-75. doi: 10.1105/tpc.112.103622. Epub 2012 Nov 27.

34.

Cohesin rings devoid of Scc3 and Pds5 maintain their stable association with the DNA.

Kulemzina I, Schumacher MR, Verma V, Reiter J, Metzler J, Failla AV, Lanz C, Sreedharan VT, Rätsch G, Ivanov D.

PLoS Genet. 2012;8(8):e1002856. doi: 10.1371/journal.pgen.1002856. Epub 2012 Aug 9.

35.

Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes.

Smith LM, Hartmann L, Drewe P, Bohnert R, Kahles A, Lanz C, Rätsch G.

RNA Biol. 2012 May;9(5):596-609. doi: 10.4161/rna.19683. Epub 2012 May 1.

PMID:
22614838
36.

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.

Preussner M, Schreiner S, Hung LH, Porstner M, Jäck HM, Benes V, Rätsch G, Bindereif A.

Nucleic Acids Res. 2012 Jul;40(12):5666-78. doi: 10.1093/nar/gks221. Epub 2012 Mar 8.

37.

Persistence and availability of Web services in computational biology.

Schultheiss SJ, Münch MC, Andreeva GD, Rätsch G.

PLoS One. 2011;6(9):e24914. doi: 10.1371/journal.pone.0024914. Epub 2011 Sep 22.

38.

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.

Nature. 2011 Aug 28;477(7365):419-23. doi: 10.1038/nature10414.

39.

RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation.

Rösel TD, Hung LH, Medenbach J, Donde K, Starke S, Benes V, Rätsch G, Bindereif A.

EMBO J. 2011 May 18;30(10):1965-76. doi: 10.1038/emboj.2011.106. Epub 2011 Apr 5.

40.

Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays.

Eichner J, Zeller G, Laubinger S, Rätsch G.

BMC Bioinformatics. 2011 Feb 16;12:55. doi: 10.1186/1471-2105-12-55.

41.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

42.

A spatial and temporal map of C. elegans gene expression.

Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J, Reinke V, Petrella L, Strome S, Von Stetina SE, Katz M, Shaham S, Rätsch G, Miller DM 3rd.

Genome Res. 2011 Feb;21(2):325-41. doi: 10.1101/gr.114595.110. Epub 2010 Dec 22.

43.

Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans.

Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM 3rd, Horvitz HR, Sternberg PW, Ringstad N.

Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):254-9. doi: 10.1073/pnas.1017354108. Epub 2010 Dec 20.

44.

RNA-Seq read alignments with PALMapper.

Jean G, Kahles A, Sreedharan VT, De Bona F, Rätsch G.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.6. doi: 10.1002/0471250953.bi1106s32.

PMID:
21154708
45.

Exploiting physico-chemical properties in string kernels.

Toussaint NC, Widmer C, Kohlbacher O, Rätsch G.

BMC Bioinformatics. 2010 Oct 26;11 Suppl 8:S7. doi: 10.1186/1471-2105-11-S8-S7.

46.

Inferring latent task structure for Multitask Learning by Multiple Kernel Learning.

Widmer C, Toussaint NC, Altun Y, Rätsch G.

BMC Bioinformatics. 2010 Oct 26;11 Suppl 8:S5. doi: 10.1186/1471-2105-11-S8-S5.

47.

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome.

Laubinger S, Zeller G, Henz SR, Buechel S, Sachsenberg T, Wang JW, Rätsch G, Weigel D.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17466-73. doi: 10.1073/pnas.1012891107. Epub 2010 Sep 24.

48.

rQuant.web: a tool for RNA-Seq-based transcript quantitation.

Bohnert R, Rätsch G.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W348-51. doi: 10.1093/nar/gkq448. Epub 2010 Jun 15.

49.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.

McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE.

Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8. doi: 10.1073/pnas.0900992106. Epub 2009 Jul 13.

50.

mGene: accurate SVM-based gene finding with an application to nematode genomes.

Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, Philips P, De Bona F, Hartmann L, Bohlen A, Krüger N, Sonnenburg S, Rätsch G.

Genome Res. 2009 Nov;19(11):2133-43. doi: 10.1101/gr.090597.108. Epub 2009 Jun 29.

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