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Items: 1 to 50 of 254

1.

Current best practices in single-cell RNA-seq analysis: a tutorial.

Luecken MD, Theis FJ.

Mol Syst Biol. 2019 Jun 19;15(6):e8746. doi: 10.15252/msb.20188746. Review.

2.

A cellular census of human lungs identifies novel cell states in health and in asthma.

Vieira Braga FA, Kar G, Berg M, Carpaij OA, Polanski K, Simon LM, Brouwer S, Gomes T, Hesse L, Jiang J, Fasouli ES, Efremova M, Vento-Tormo R, Talavera-López C, Jonker MR, Affleck K, Palit S, Strzelecka PM, Firth HV, Mahbubani KT, Cvejic A, Meyer KB, Saeb-Parsy K, Luinge M, Brandsma CA, Timens W, Angelidis I, Strunz M, Koppelman GH, van Oosterhout AJ, Schiller HB, Theis FJ, van den Berge M, Nawijn MC, Teichmann SA.

Nat Med. 2019 Jun 17. doi: 10.1038/s41591-019-0468-5. [Epub ahead of print]

PMID:
31209336
3.

Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns.

Czamara D, Eraslan G, Page CM, Lahti J, Lahti-Pulkkinen M, Hämäläinen E, Kajantie E, Laivuori H, Villa PM, Reynolds RM, Nystad W, Håberg SE, London SJ, O'Donnell KJ, Garg E, Meaney MJ, Entringer S, Wadhwa PD, Buss C, Jones MJ, Lin DTS, MacIsaac JL, Kobor MS, Koen N, Zar HJ, Koenen KC, Dalvie S, Stein DJ, Kondofersky I, Müller NS, Theis FJ; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Räikkönen K, Binder EB.

Nat Commun. 2019 Jun 11;10(1):2548. doi: 10.1038/s41467-019-10461-0.

4.

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.

Bastidas-Ponce A, Tritschler S, Dony L, Scheibner K, Tarquis-Medina M, Salinno C, Schirge S, Burtscher I, Böttcher A, Theis FJ, Lickert H, Bakhti M.

Development. 2019 Jun 17;146(12). pii: dev173849. doi: 10.1242/dev.173849.

PMID:
31160421
5.

Dynamic modelling of an ACADS genotype in fatty acid oxidation - Application of cellular models for the analysis of common genetic variants.

Matejka K, Stückler F, Salomon M, Ensenauer R, Reischl E, Hoerburger L, Grallert H, Kastenmüller G, Peters A, Daniel H, Krumsiek J, Theis FJ, Hauner H, Laumen H.

PLoS One. 2019 May 23;14(5):e0216110. doi: 10.1371/journal.pone.0216110. eCollection 2019.

6.

A map of β-cell differentiation pathways supports cell therapies for diabetes.

Theis FJ, Lickert H.

Nature. 2019 May;569(7756):342-343. doi: 10.1038/d41586-019-01211-9. No abstract available.

PMID:
31076731
7.

Altered relaxation times in MRI indicate bronchopulmonary dysplasia.

Förster K, Ertl-Wagner B, Ehrhardt H, Busen H, Sass S, Pomschar A, Naehrlich L, Schulze A, Flemmer AW, Hübener C, Eickelberg O, Theis F, Dietrich O, Hilgendorff A.

Thorax. 2019 May 2. pii: thoraxjnl-2018-212384. doi: 10.1136/thoraxjnl-2018-212384. [Epub ahead of print]

PMID:
31048507
8.

Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity - indications of immune cell activation.

Laimighofer M, Lickert R, Fuerst R, Theis FJ, Winkler C, Bonifacio E, Ziegler AG, Krumsiek J.

Sci Rep. 2019 Apr 18;9(1):6250. doi: 10.1038/s41598-019-42750-5.

9.

The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease.

Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga F, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis FJ, Regev A, Kaminski N, Rajagopal J, Teichmann SA, Misharin AV, Nawijn MC.

Am J Respir Cell Mol Biol. 2019 Apr 17. doi: 10.1165/rcmb.2018-0416TR. [Epub ahead of print]

PMID:
30995076
10.

Deep learning: new computational modelling techniques for genomics.

Eraslan G, Avsec Ž, Gagneur J, Theis FJ.

Nat Rev Genet. 2019 Jul;20(7):389-403. doi: 10.1038/s41576-019-0122-6. Review.

PMID:
30971806
11.

Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data.

Hross S, Theis FJ, Sixt M, Hasenauer J.

J R Soc Interface. 2018 Dec 21;15(149):20180600. doi: 10.1098/rsif.2018.0600.

12.

Inferring population dynamics from single-cell RNA-sequencing time series data.

Fischer DS, Fiedler AK, Kernfeld EM, Genga RMJ, Bastidas-Ponce A, Bakhti M, Lickert H, Hasenauer J, Maehr R, Theis FJ.

Nat Biotechnol. 2019 Apr;37(4):461-468. doi: 10.1038/s41587-019-0088-0. Epub 2019 Apr 1.

PMID:
30936567
13.

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.

Wolf FA, Hamey FK, Plass M, Solana J, Dahlin JS, Göttgens B, Rajewsky N, Simon L, Theis FJ.

Genome Biol. 2019 Mar 19;20(1):59. doi: 10.1186/s13059-019-1663-x.

14.

Erratum: Publisher Correction: Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection.

Fröhlich F, Reiser A, Fink L, Woschée D, Ligon T, Theis FJ, Rädler JO, Hasenauer J.

NPJ Syst Biol Appl. 2019 Mar 7;5:11. doi: 10.1038/s41540-019-0083-6. eCollection 2019.

15.

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies.

Do KT, Wahl S, Raffler J, Molnos S, Laimighofer M, Adamski J, Suhre K, Strauch K, Peters A, Gieger C, Langenberg C, Stewart ID, Theis FJ, Grallert H, Kastenmüller G, Krumsiek J.

Metabolomics. 2018 Sep 20;14(10):128. doi: 10.1007/s11306-018-1420-2.

16.

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics.

Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, Tsitsiridis G, Ansari M, Graf E, Strom TM, Nagendran M, Desai T, Eickelberg O, Mann M, Theis FJ, Schiller HB.

Nat Commun. 2019 Feb 27;10(1):963. doi: 10.1038/s41467-019-08831-9.

17.

A strategy for high-dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors.

Krautenbacher N, Flach N, Böck A, Laubhahn K, Laimighofer M, Theis FJ, Ankerst DP, Fuchs C, Schaub B.

Allergy. 2019 Feb 9. doi: 10.1111/all.13745. [Epub ahead of print]

PMID:
30737985
18.

Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine.

Kaderali L, Theis F, Ganusov VV, Ciupe SM, Mehr R, Ribeiro RM, Hernandez-Vargas EA.

Front Microbiol. 2019 Jan 23;9:3338. doi: 10.3389/fmicb.2018.03338. eCollection 2018. No abstract available.

19.

IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling.

Sheng X, Nenseth HZ, Qu S, Kuzu OF, Frahnow T, Simon L, Greene S, Zeng Q, Fazli L, Rennie PS, Mills IG, Danielsen H, Theis F, Patterson JB, Jin Y, Saatcioglu F.

Nat Commun. 2019 Jan 24;10(1):323. doi: 10.1038/s41467-018-08152-3.

20.

Single-cell RNA-seq denoising using a deep count autoencoder.

Eraslan G, Simon LM, Mircea M, Mueller NS, Theis FJ.

Nat Commun. 2019 Jan 23;10(1):390. doi: 10.1038/s41467-018-07931-2.

21.

A test metric for assessing single-cell RNA-seq batch correction.

Büttner M, Miao Z, Wolf FA, Teichmann SA, Theis FJ.

Nat Methods. 2019 Jan;16(1):43-49. doi: 10.1038/s41592-018-0254-1. Epub 2018 Dec 20.

PMID:
30573817
22.

Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis.

Bast L, Calzolari F, Strasser MK, Hasenauer J, Theis FJ, Ninkovic J, Marr C.

Cell Rep. 2018 Dec 18;25(12):3231-3240.e8. doi: 10.1016/j.celrep.2018.11.088.

23.

Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection.

Fröhlich F, Reiser A, Fink L, Woschée D, Ligon T, Theis FJ, Rädler JO, Hasenauer J.

NPJ Syst Biol Appl. 2018 Dec 10;5:1. doi: 10.1038/s41540-018-0079-7. eCollection 2019. Erratum in: NPJ Syst Biol Appl. 2019 Mar 7;5:11.

24.

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model.

Fröhlich F, Kessler T, Weindl D, Shadrin A, Schmiester L, Hache H, Muradyan A, Schütte M, Lim JH, Heinig M, Theis FJ, Lehrach H, Wierling C, Lange B, Hasenauer J.

Cell Syst. 2018 Dec 26;7(6):567-579.e6. doi: 10.1016/j.cels.2018.10.013. Epub 2018 Nov 28.

25.

Impact of Brain Fatty Acid Signaling on Peripheral Insulin Action in Mice.

Neschen S, Wu M, Fuchs C, Kondofersky I, Theis FJ, de Angelis MH, Häring HU, Sartorius T.

Exp Clin Endocrinol Diabetes. 2018 Nov 5. doi: 10.1055/a-0735-9533. [Epub ahead of print]

PMID:
30396212
26.

Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?

Pitea A, Kondofersky I, Sass S, Theis FJ, Mueller NS, Unger K.

Brief Bioinform. 2018 Oct 23. doi: 10.1093/bib/bby096. [Epub ahead of print]

PMID:
30351397
27.

Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate.

Tischler J, Gruhn WH, Reid J, Allgeyer E, Buettner F, Marr C, Theis F, Simons BD, Wernisch L, Surani MA.

EMBO J. 2019 Jan 3;38(1). pii: e99518. doi: 10.15252/embj.201899518. Epub 2018 Sep 26.

28.

Impulse model-based differential expression analysis of time course sequencing data.

Fischer DS, Theis FJ, Yosef N.

Nucleic Acids Res. 2018 Nov 16;46(20):e119. doi: 10.1093/nar/gky675.

29.

Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm.

Strasser MK, Hoppe PS, Loeffler D, Kokkaliaris KD, Schroeder T, Theis FJ, Marr C.

Nat Commun. 2018 Jul 12;9(1):2697. doi: 10.1038/s41467-018-05037-3.

30.

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

Ballnus B, Schaper S, Theis FJ, Hasenauer J.

Bioinformatics. 2018 Jul 1;34(13):i494-i501. doi: 10.1093/bioinformatics/bty229.

31.

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 1;7(6). doi: 10.1093/gigascience/giy070.

32.

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. 2019 Jan;33(1):115-122. doi: 10.1111/jdv.15101. Epub 2018 Jul 2.

PMID:
29856508
33.

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 Jul 10;11(1):58-69. doi: 10.1016/j.stemcr.2018.04.019. Epub 2018 May 17.

34.

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
35.

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 Aug;138(8):1785-1794. doi: 10.1016/j.jid.2018.02.034. Epub 2018 Mar 9.

PMID:
29526761
36.

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.

37.

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.

38.

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.

39.

Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin.

Stirm L, Huypens P, Sass S, Batra R, Fritsche L, Brucker S, Abele H, Hennige AM, Theis F, Beckers J, Hrabě de Angelis M, Fritsche A, Häring HU, Staiger H.

Sci Rep. 2018 Jan 22;8(1):1366. doi: 10.1038/s41598-018-19200-9.

40.

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.

41.

Lifetime study in mice after acute low-dose ionizing radiation: a multifactorial study with special focus on cataract risk.

Dalke C, Neff F, Bains SK, Bright S, Lord D, Reitmeir P, Rößler U, Samaga D, Unger K, Braselmann H, Wagner F, Greiter M, Gomolka M, Hornhardt S, Kunze S, Kempf SJ, Garrett L, Hölter SM, Wurst W, Rosemann M, Azimzadeh O, Tapio S, Aubele M, Theis F, Hoeschen C, Slijepcevic P, Kadhim M, Atkinson M, Zitzelsberger H, Kulka U, Graw J.

Radiat Environ Biophys. 2018 May;57(2):99-113. doi: 10.1007/s00411-017-0728-z. Epub 2018 Jan 11.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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
49.

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.

50.

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.

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