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Items: 1 to 50 of 166

1.

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data.

Simon LM, Karg S, Westermann AJ, Engel M, Elbehery AHA, Hense B, Heinig M, Deng L, Theis FJ.

Gigascience. 2018 Jun 12. doi: 10.1093/gigascience/giy070. [Epub ahead of print]

PMID:
29901703
2.

Is the humoral immunity dispensable for the pathogenesis of psoriasis?

Thomas J, Küpper M, Batra R, Jargosch M, Atenhan A, Baghin V, Krause L, Lauffer F, Biedermann T, Theis FJ, Eyerich K, Eyerich S, Garzorz-Stark N.

J Eur Acad Dermatol Venereol. 2018 Jun 1. doi: 10.1111/jdv.15101. [Epub ahead of print]

PMID:
29856508
3.

Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells.

Hastreiter S, Skylaki S, Loeffler D, Reimann A, Hilsenbeck O, Hoppe PS, Coutu DL, Kokkaliaris KD, Schwarzfischer M, Anastassiadis K, Theis FJ, Schroeder T.

Stem Cell Reports. 2018 May 10. pii: S2213-6711(18)30187-5. doi: 10.1016/j.stemcr.2018.04.019. [Epub ahead of print]

4.

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.

Plass M, Solana J, Wolf FA, Ayoub S, Misios A, Glažar P, Obermayer B, Theis FJ, Kocks C, Rajewsky N.

Science. 2018 May 25;360(6391). pii: eaaq1723. doi: 10.1126/science.aaq1723. Epub 2018 Apr 19.

PMID:
29674432
5.

Type I Immune Response Induces Keratinocyte Necroptosis and Is Associated with Interface Dermatitis.

Lauffer F, Jargosch M, Krause L, Garzorz-Stark N, Franz R, Roenneberg S, Böhner A, Mueller NS, Theis FJ, Schmidt-Weber CB, Biedermann T, Eyerich S, Eyerich K.

J Invest Dermatol. 2018 Mar 9. pii: S0022-202X(18)30215-X. doi: 10.1016/j.jid.2018.02.034. [Epub ahead of print]

PMID:
29526761
6.

Whither systems medicine?

Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O.

Exp Mol Med. 2018 Mar 2;50(3):e453. doi: 10.1038/emm.2017.290. Review.

7.

Publisher Correction: Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway.

Benedetti E, Pučić-Baković M, Keser T, Wahl A, Hassinen A, Yang JY, Liu L, Trbojević-Akmačić I, Razdorov G, Štambuk J, Klarić L, Ugrina I, Selman MHJ, Wuhrer M, Rudan I, Polasek O, Hayward C, Grallert H, Strauch K, Peters A, Meitinger T, Gieger C, Vilaj M, Boons GJ, Moremen KW, Ovchinnikova T, Bovin N, Kellokumpu S, Theis FJ, Lauc G, Krumsiek J.

Nat Commun. 2018 Feb 13;9(1):706. doi: 10.1038/s41467-017-02379-2.

8.

SCANPY: large-scale single-cell gene expression data analysis.

Wolf FA, Angerer P, Theis FJ.

Genome Biol. 2018 Feb 6;19(1):15. doi: 10.1186/s13059-017-1382-0.

9.

Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients.

González-Vallinas M, Rodríguez-Paredes M, Albrecht M, Sticht C, Stichel D, Gutekunst J, Pitea A, Sass S, Sánchez-Rivera FJ, Lorenzo-Bermejo J, Schmitt J, De La Torre C, Warth A, Theis FJ, Müller NS, Gretz N, Muley T, Meister M, Tschaharganeh DF, Schirmacher P, Matthäus F, Breuhahn K.

Mol Cancer Res. 2018 Mar;16(3):390-402. doi: 10.1158/1541-7786.MCR-17-0334. Epub 2018 Jan 12.

PMID:
29330288
10.

Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies.

Krautenbacher N, Theis FJ, Fuchs C.

Comput Math Methods Med. 2017;2017:7847531. doi: 10.1155/2017/7847531. Epub 2017 Sep 24.

11.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

12.

Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway.

Benedetti E, Pučić-Baković M, Keser T, Wahl A, Hassinen A, Yang JY, Liu L, Trbojević-Akmačić I, Razdorov G, Štambuk J, Klarić L, Ugrina I, Selman MHJ, Wuhrer M, Rudan I, Polasek O, Hayward C, Grallert H, Strauch K, Peters A, Meitinger T, Gieger C, Vilaj M, Boons GJ, Moremen KW, Ovchinnikova T, Bovin N, Kellokumpu S, Theis FJ, Lauc G, Krumsiek J.

Nat Commun. 2017 Nov 14;8(1):1483. doi: 10.1038/s41467-017-01525-0. Erratum in: Nat Commun. 2018 Feb 13;9(1):706.

13.

GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency.

Krendl C, Shaposhnikov D, Rishko V, Ori C, Ziegenhain C, Sass S, Simon L, Müller NS, Straub T, Brooks KE, Chavez SL, Enard W, Theis FJ, Drukker M.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9579-E9588. doi: 10.1073/pnas.1708341114. Epub 2017 Oct 25.

14.

netReg: network-regularized linear models for biological association studies.

Dirmeier S, Fuchs C, Mueller NS, Theis FJ.

Bioinformatics. 2018 Mar 1;34(5):896-898. doi: 10.1093/bioinformatics/btx677.

PMID:
29077797
15.

Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib.

Sobotta S, Raue A, Huang X, Vanlier J, Jünger A, Bohl S, Albrecht U, Hahnel MJ, Wolf S, Mueller NS, D'Alessandro LA, Mueller-Bohl S, Boehm ME, Lucarelli P, Bonefas S, Damm G, Seehofer D, Lehmann WD, Rose-John S, van der Hoeven F, Gretz N, Theis FJ, Ehlting C, Bode JG, Timmer J, Schilling M, Klingmüller U.

Front Physiol. 2017 Oct 9;8:775. doi: 10.3389/fphys.2017.00775. eCollection 2017.

16.

Early Identification of Bronchopulmonary Dysplasia Using Novel Biomarkers by Proteomic Screening.

Förster K, Sass S, Ehrhardt H, Mous DS, Rottier RJ, Oak P, Schulze A, Flemmer AW, Gronbach J, Hübener C, Desai T, Eickelberg O, Theis FJ, Hilgendorff A.

Am J Respir Crit Care Med. 2018 Apr 15;197(8):1076-1080. doi: 10.1164/rccm.201706-1218LE. No abstract available.

PMID:
29053024
17.

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms.

Molnos S, Baumbach C, Wahl S, Müller-Nurasyid M, Strauch K, Wang-Sattler R, Waldenberger M, Meitinger T, Adamski J, Kastenmüller G, Suhre K, Peters A, Grallert H, Theis FJ, Gieger C.

BMC Bioinformatics. 2017 Sep 29;18(1):429. doi: 10.1186/s12859-017-1838-y.

18.

Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas.

Tritschler S, Theis FJ, Lickert H, Böttcher A.

Mol Metab. 2017 Jul 20;6(9):974-990. doi: 10.1016/j.molmet.2017.06.021. eCollection 2017 Sep. Review.

19.

Toll-like receptor 7/8 agonists stimulate plasmacytoid dendritic cells to initiate TH17-deviated acute contact dermatitis in human subjects.

Garzorz-Stark N, Lauffer F, Krause L, Thomas J, Atenhan A, Franz R, Roenneberg S, Boehner A, Jargosch M, Batra R, Mueller NS, Haak S, Groß C, Groß O, Traidl-Hoffmann C, Theis FJ, Schmidt-Weber CB, Biedermann T, Eyerich S, Eyerich K.

J Allergy Clin Immunol. 2018 Apr;141(4):1320-1333.e11. doi: 10.1016/j.jaci.2017.07.045. Epub 2017 Sep 19.

20.

A scalable moment-closure approximation for large-scale biochemical reaction networks.

Kazeroonian A, Theis FJ, Hasenauer J.

Bioinformatics. 2017 Jul 15;33(14):i293-i300. doi: 10.1093/bioinformatics/btx249.

21.

Reconstructing cell cycle and disease progression using deep learning.

Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, Wolf FA.

Nat Commun. 2017 Sep 6;8(1):463. doi: 10.1038/s41467-017-00623-3.

22.

Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young.

Frohnert BI, Laimighofer M, Krumsiek J, Theis FJ, Winkler C, Norris JM, Ziegler AG, Rewers MJ, Steck AK.

Pediatr Diabetes. 2018 Mar;19(2):277-283. doi: 10.1111/pedi.12543. Epub 2017 Jul 11.

PMID:
28695611
23.

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems.

Ballnus B, Hug S, Hatz K, Görlitz L, Hasenauer J, Theis FJ.

BMC Syst Biol. 2017 Jun 24;11(1):63. doi: 10.1186/s12918-017-0433-1.

24.

A BaSiC tool for background and shading correction of optical microscopy images.

Peng T, Thorn K, Schroeder T, Wang L, Theis FJ, Marr C, Navab N.

Nat Commun. 2017 Jun 8;8:14836. doi: 10.1038/ncomms14836.

25.

Model-based branching point detection in single-cell data by K-branches clustering.

Chlis NK, Wolf FA, Theis FJ.

Bioinformatics. 2017 Oct 15;33(20):3211-3219. doi: 10.1093/bioinformatics/btx325.

26.

Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach.

Milger K, Götschke J, Krause L, Nathan P, Alessandrini F, Tufman A, Fischer R, Bartel S, Theis FJ, Behr J, Dehmel S, Mueller NS, Kneidinger N, Krauss-Etschmann S.

Allergy. 2017 Dec;72(12):1962-1971. doi: 10.1111/all.13205. Epub 2017 Jun 19.

PMID:
28513859
27.

Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma.

Bartel S, Schulz N, Alessandrini F, Schamberger AC, Pagel P, Theis FJ, Milger K, Noessner E, Stick SM, Kicic A, Eickelberg O, Freishtat RJ, Krauss-Etschmann S.

Sci Rep. 2017 Apr 6;7:46026. doi: 10.1038/srep46026.

28.

fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy.

Hilsenbeck O, Schwarzfischer M, Loeffler D, Dimopoulos S, Hastreiter S, Marr C, Theis FJ, Schroeder T.

Bioinformatics. 2017 Jul 1;33(13):2020-2028. doi: 10.1093/bioinformatics/btx107.

PMID:
28334115
29.

Prospective identification of hematopoietic lineage choice by deep learning.

Buggenthin F, Buettner F, Hoppe PS, Endele M, Kroiss M, Strasser M, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Schroeder T, Theis FJ, Marr C.

Nat Methods. 2017 Apr;14(4):403-406. doi: 10.1038/nmeth.4182. Epub 2017 Feb 20.

30.

Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma.

Florea AM, Varghese E, McCallum JE, Mahgoub S, Helmy I, Varghese S, Gopinath N, Sass S, Theis FJ, Reifenberger G, Büsselberg D.

Oncotarget. 2017 Apr 4;8(14):22876-22893. doi: 10.18632/oncotarget.15283.

31.

cgCorrect: a method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics.

Blasi T, Buettner F, Strasser MK, Marr C, Theis FJ.

Phys Biol. 2017 May 11;14(3):036001. doi: 10.1088/1478-3975/aa609a.

PMID:
28198357
32.

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.

Fröhlich F, Kaltenbacher B, Theis FJ, Hasenauer J.

PLoS Comput Biol. 2017 Jan 23;13(1):e1005331. doi: 10.1371/journal.pcbi.1005331. eCollection 2017 Jan.

33.

Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models.

Jagiella N, Rickert D, Theis FJ, Hasenauer J.

Cell Syst. 2017 Feb 22;4(2):194-206.e9. doi: 10.1016/j.cels.2016.12.002. Epub 2017 Jan 11.

34.

Parameter estimation for dynamical systems with discrete events and logical operations.

Fröhlich F, Theis FJ, Rädler JO, Hasenauer J.

Bioinformatics. 2017 Apr 1;33(7):1049-1056. doi: 10.1093/bioinformatics/btw764.

PMID:
28040696
35.

Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells.

Feigelman J, Ganscha S, Hastreiter S, Schwarzfischer M, Filipczyk A, Schroeder T, Theis FJ, Marr C, Claassen M.

Cell Syst. 2016 Nov 23;3(5):480-490.e13. doi: 10.1016/j.cels.2016.11.001.

36.

Inferring catalysis in biological systems.

Kondofersky I, Theis FJ, Fuchs C.

IET Syst Biol. 2016 Dec;10(6):210-218. doi: 10.1049/iet-syb.2015.0087.

PMID:
27879475
37.

Peptide serum markers in islet autoantibody-positive children.

von Toerne C, Laimighofer M, Achenbach P, Beyerlein A, de Las Heras Gala T, Krumsiek J, Theis FJ, Ziegler AG, Hauck SM.

Diabetologia. 2017 Feb;60(2):287-295. doi: 10.1007/s00125-016-4150-x. Epub 2016 Nov 4.

PMID:
27815605
38.

Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy.

Kong B, Bruns P, Behler NA, Chang L, Schlitter AM, Cao J, Gewies A, Ruland J, Fritzsche S, Valkovskaya N, Jian Z, Regel I, Raulefs S, Irmler M, Beckers J, Friess H, Erkan M, Mueller NS, Roth S, Hackert T, Esposito I, Theis FJ, Kleeff J, Michalski CW.

Gut. 2018 Jan;67(1):146-156. doi: 10.1136/gutjnl-2015-310913. Epub 2016 Sep 19.

PMID:
27646934
39.

TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus.

Senís E, Mockenhaupt S, Rupp D, Bauer T, Paramasivam N, Knapp B, Gronych J, Grosse S, Windisch MP, Schmidt F, Theis FJ, Eils R, Lichter P, Schlesner M, Bartenschlager R, Grimm D.

Nucleic Acids Res. 2017 Jan 9;45(1):e3. doi: 10.1093/nar/gkw805. Epub 2016 Sep 9.

40.

Diffusion pseudotime robustly reconstructs lineage branching.

Haghverdi L, Büttner M, Wolf FA, Buettner F, Theis FJ.

Nat Methods. 2016 Oct;13(10):845-8. doi: 10.1038/nmeth.3971. Epub 2016 Aug 29.

PMID:
27571553
41.

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.

Fiedler A, Raeth S, Theis FJ, Hausser A, Hasenauer J.

BMC Syst Biol. 2016 Aug 22;10(1):80. doi: 10.1186/s12918-016-0319-7.

42.

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.

Fröhlich F, Thomas P, Kazeroonian A, Theis FJ, Grima R, Hasenauer J.

PLoS Comput Biol. 2016 Jul 22;12(7):e1005030. doi: 10.1371/journal.pcbi.1005030. eCollection 2016 Jul.

43.

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.

Hoppe PS, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Moritz N, Endele M, Filipczyk A, Gambardella A, Ahmed N, Etzrodt M, Coutu DL, Rieger MA, Marr C, Strasser MK, Schauberger B, Burtscher I, Ermakova O, Bürger A, Lickert H, Nerlov C, Theis FJ, Schroeder T.

Nature. 2016 Jul 14;535(7611):299-302. doi: 10.1038/nature18320.

PMID:
27411635
44.

Software tools for single-cell tracking and quantification of cellular and molecular properties.

Hilsenbeck O, Schwarzfischer M, Skylaki S, Schauberger B, Hoppe PS, Loeffler D, Kokkaliaris KD, Hastreiter S, Skylaki E, Filipczyk A, Strasser M, Buggenthin F, Feigelman JS, Krumsiek J, van den Berg AJ, Endele M, Etzrodt M, Marr C, Theis FJ, Schroeder T.

Nat Biotechnol. 2016 Jul 12;34(7):703-6. doi: 10.1038/nbt.3626. No abstract available.

PMID:
27404877
45.

A computational model to predict severity of atopic eczema from 30 serum proteins.

Krause L, Mourantchanian V, Brockow K, Theis FJ, Schmidt-Weber CB, Knapp B, Mueller NS, Eyerich S.

J Allergy Clin Immunol. 2016 Oct;138(4):1207-1210.e2. doi: 10.1016/j.jaci.2016.04.018. Epub 2016 May 13. No abstract available. Erratum in: J Allergy Clin Immunol. 2017 Mar;139(3):1068-1069.

PMID:
27315765
46.

A novel molecular disease classifier for psoriasis and eczema.

Garzorz-Stark N, Krause L, Lauffer F, Atenhan A, Thomas J, Stark SP, Franz R, Weidinger S, Balato A, Mueller NS, Theis FJ, Ring J, Schmidt-Weber CB, Biedermann T, Eyerich S, Eyerich K.

Exp Dermatol. 2016 Oct;25(10):767-74. doi: 10.1111/exd.13077.

PMID:
27193975
47.

Editorial overview: Systems biology-the intersection of experiments and computation, underpinning biotechnology.

Styczynski MP, Theis FJ.

Curr Opin Biotechnol. 2016 Jun;39:iv-vi. doi: 10.1016/j.copbio.2016.04.025. Epub 2016 May 9. No abstract available.

PMID:
27173375
48.

MEMO: multi-experiment mixture model analysis of censored data.

Geissen EM, Hasenauer J, Heinrich S, Hauf S, Theis FJ, Radde NE.

Bioinformatics. 2016 Aug 15;32(16):2464-72. doi: 10.1093/bioinformatics/btw190. Epub 2016 Apr 19.

49.

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

Blasi T, Feller C, Feigelman J, Hasenauer J, Imhof A, Theis FJ, Becker PB, Marr C.

Cell Syst. 2016 Jan 27;2(1):49-58. doi: 10.1016/j.cels.2016.01.002. Epub 2016 Jan 27.

50.

Computational approaches for systems metabolomics.

Krumsiek J, Bartel J, Theis FJ.

Curr Opin Biotechnol. 2016 Jun;39:198-206. doi: 10.1016/j.copbio.2016.04.009. Epub 2016 Apr 30. Review.

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