Stefanie Widder Paper 24


Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation. S Widder, I Goerzer, B Friedel et al. and E. Puchammer-Stoeckl Microbiome 2022




Stefanie Widder Paper 23


Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways. S Widder, J Zhao, L Carmody, et al. and J J LiPuma. ISMEJ 2021




Stefanie Widder Paper 22


Multi-omics profiling predicts allograft function after lung transplantations. M Watzenboeck, A Gorki, F Quattrone, R Gawish et al. and S Widder & S Knapp. European Respiratory Journal 2021




Stefanie Widder Paper 21


Editorial: Microbial Metabolites in Cystic Fibrosis: A Target for Future Therapy? S Widder and S Knapp. American Journal of Respiratory Cell and Molecular Biology 2019




Stefanie Widder Paper 20


Signatures of ecological processes in microbial community time series. K Faust, F Bauchinger, B Laroche, S de Buyl, L Lahti, A Washburne, D Gonze and S Widder. Microbiome 2018




Stefanie Widder Paper 1


Using metabolic networks to resolve ecological properties of microbiomes. E Muller, K Faust, S Widder, M Herold, S Martinez Abas and P Wilmes. Cur Opin Sys Biol. 2017




Stefanie Widder Paper 2

Ecological networking of cystic fibrosis lung infections. Quinn RA, Whiteson K, Lim YW, Zhao J, Conrad D, LiPuma JJ, Rohwer F, Widder S. NPJ Biofilms Microbiomes. 2016 Dec




Stefanie Widder Paper 3
The origin and evolution of cell types. Arendt D*, Musser JM*, Baker CVH, Bergman A, Cepko C, Erwin DH, Pavlicev M, Schlosser G, Widder S, Laubichler MD, Wagner GP. Nat Rev Genet. 2016 Dec

News and Features:
Science (350/2015): In depth-Using evolution to better identify cell types



Stefanie Widder Paper 4Challenges in microbial ecology: building predictive understanding of community function and dynamics. Widder S, Allen R, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Isaac Newton Institute Fellows, Soyer OS. ISME J. 2016 Nov


Stefanie Widder Paper 5


Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens. Luter HM, Widder S, Botté ES, Abdul Wahab M, Whalan S, Moitinho-Silva L, Thomas T, Webster NS. PeerJ. 2015 Dec





Stefanie Widder Paper 6

Wiring for Independence: Positive Feedback Motifs Facilitate Individuation of Traits in Development and Evolution. Pavlicev M, Widder S. J Exp Zool B Mol Dev Evol. 2015 Mar





Stefanie Widder Paper 7


Fluvial network organization imprints on microbial co-occurrence networks. Widder S, Besemer K, Singer GA, Ceola S, Bertuzzo E, Quince C, Sloan WT, Rinaldo A, Battin TJ. Proc Natl Acad Sci U S A. 2014 Sep

News and Features:
PNAS (111/2014): This week in PNAS



Stefanie Widder Paper 8Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman. Maixner F*, Thomma A*, Cipollini G, Widder S, Rattei T, Zink A. PLoS One. 2014 Jun
News and Features:
Der Kurier, Printversion (16/7/2014): Schon Ötzi wurde von Zahnfleischentzündung gequält.
Der Standard (16/7/2014): Ötzis Knochenanalyse enthüllt "nichtmenschliche" DNA
Universität Wien - uni:view magazin (15/7/2014): Ötzis "nichtmenschliche" DNA entschlüsselt


Stefanie Widder Paper 9


Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Berry D, Widder S. Front Microbiol. 2014 May




Stefanie Widder Paper 10

Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs. Behrens S, Widder S, Mannala GK, Qing X, Madhugiri R, Kefer N, Abu Mraheil M, Rattei T, Hain T. PLoS One. 2014 Feb




Stefanie Widder Paper 11


Evolvability of feed-forward loop architecture biases its abundance in transcription networks. Widder S, Solé R, Macía J. BMC Syst Biol. 2012 Jan



Stefanie Widder Paper 12


Specialized or flexible feed-forward loop motifs: a question of topology. Macía J*, Widder S*, Solé R. BMC Syst Biol. 2009 Aug




Stefanie Widder Paper 13


Why are cellular switches Boolean? General conditions for multistable genetic circuits. Macía J, Widder S, Solé R. J Theor Biol. 2009 Nov




Stefanie Widder Paper 14


Monomeric bistability and the role of autoloops in gene regulation. Widder S*, Macía J*, Solé R. PLoS One. 2009





Stefanie Widder Paper 15

Dynamic patterns of gene regulation I: simple two-gene systems. Widder S, Schicho J, Schuster P. Front Microbiol. 2014 May




Stefanie Widder Paper 16

A minimal and self-consistent in silico cell model based on macromolecular interactions. Flamm C, Endler L, Müller S, Widder S, Schuster P. Philos Trans R Soc Lond B Biol Sci. 2007 Oct




Stefanie Widder Paper 17

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C. Bioinformatics. 2006 Jun




Stefanie Widder Paper 18


A generalized model of the repressilator. Müller S, Hofbauer J, Endler L, Flamm C, Widder S, Schuster P. Journal Math Biol. 2006 Dec




Stefanie Widder Paper 19


p59OASL, a 24–54 oligoadenylate synthetase like protein: a novel human gene related to the 24–54 oligoadenylate synthetase family. Hartmann R, Olsen HS, Widder S, Jørgensen R, Justesen J. Nucleic Acids Research, 1998