, 2023. Using protein-per-mRNA differences among human tissues in codon optimization. Genome Biol 24(1):34
, 2023. Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Res 51(3):e17
, 2023. Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms. Nat Biotechnol.
, 2023. Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation. Mol Syst Biol 19(1):e11037
, 2022. Chromosome segregation fidelity requires microtubule polyglutamylation by the cancer downregulated enzyme TTLL11. Nat Commun 13(1):7147
, 2022. SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome. Nucleic Acids Res 50(22):e127
, 2022. MycoWiki: Functional annotation of the minimal model organism Mycoplasma pneumoniae. Front Microbiol 13:935066
, 2022. Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision. Proc Natl Acad Sci U S A 119(29):e2117090119
, 2022. pyFoldX: enabling biomolecular analysis and engineering along structural ensembles. Bioinformatics 38(8):2353-2355
, 2022. robustica: customizable robust independent component analysis. BMC Bioinformatics 23(1):519
, 2021. Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers. PLoS Biol 19(2):e3001138
, 2021. Lox'd in translation: contradictions in the nomenclature surrounding common lox-site mutants and their implications in experiments. Microbiology (Reading) 167.
, 2021. LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions. Microb Biotechnol 14(6):2403-2419
, 2021. A RAC-GEF network critical for early intestinal tumourigenesis. Nat Commun 12(1):56
, 2021. Protein haploinsufficiency drivers identify MYBPC3 variants that cause hypertrophic cardiomyopathy. J Biol Chem 297(1):100854
, 2021. Translational adaptation of human viruses to the tissues they infect. Cell Rep 34(11):108872
, 2021. Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control. iScience 24(9):102985
, 2021. Functional Characterization of the Cell Division Gene Cluster of the Wall-less Bacterium Mycoplasma genitalium. Front Microbiol 12:695572
, 2021. Engineering a genome-reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo. Mol Syst Biol 17(10):e10145
, 2020. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS(G13D). Nat Commun 11(1):499
, 2020. Translational efficiency across healthy and tumor tissues is proliferation-related. Mol Syst Biol 16(3):e9275
, 2020. ProteinFishing: a protein complex generator within the ModelX toolsuite. Bioinformatics 36(14):4208-4210
, 2020. Impact of C-terminal amino acid composition on protein expression in bacteria. Mol Syst Biol 16(5):e9208
, 2020. Inferring Active Metabolic Pathways from Proteomics and Essentiality Data. Cell Rep 31(9):107722
, 2020. Characterization of different alginate lyases for dissolving Pseudomonas aeruginosa biofilms. Sci Rep 10(1):9390
, 2020. Mycoplasma pneumoniae Genome Editing Based on Oligo Recombineering and Cas9-Mediated Counterselection. ACS Synth Biol 9(7):1693-1704
, 2020. Protein quality control and regulated proteolysis in the genome-reduced organism Mycoplasma pneumoniae. Mol Syst Biol 16(12):e9530
, 2020. FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies. Nucleic Acids Res 48(17):e102
, 2020. Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media. NPJ Syst Biol Appl 6(1):33
, 2020. In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species. PLoS Comput Biol 16(12):e1008450
, 2020. Mutation bias within oncogene families is related to proliferation-specific codon usage. Proc Natl Acad Sci U S A 117(48):30848-30856
, 2019. Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors. Cell Syst 9(2):143-158.e13
, 2019. The role of clonal communication and heterogeneity in breast cancer. BMC Cancer 19(1):666
, 2019. SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes. DNA Res 26(4):327-339
, 2019. FoldX 5.0: working with RNA, small molecules and a new graphical interface. Bioinformatics 35(20):4168-4169
, 2019. Unraveling the hidden universe of small proteins in bacterial genomes. Mol Syst Biol 15(2):e8290
, 2018. VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants. Front Genet 9:620
, 2018. rec-YnH enables simultaneous many-by-many detection of direct protein-protein and protein-RNA interactions. Nat Commun 9(1):3747
, 2018. Systems level expression correlation of Ras GTPase regulators. Cell Commun Signal 16(1):46
, 2018. Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates. Nucleic Acids Res 46(14):7022-7039
, 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biol 19(1):67
, 2018. FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1). Nucleic Acids Res 46(8):3852-3863
, 2018. Generation of rationally-designed nerve growth factor (NGF) variants with receptor specificity. Biochem Biophys Res Commun 495(1):700-705
, 2017. A Comprehensive View of the β-Arrestinome. Front Endocrinol (Lausanne) 8:32
, 2017. Simple and complex retinal dystrophies are associated with profoundly different disease networks. Sci Rep 7:41835
, 2017. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae. Nat Commun 8:14665
, 2017. Interaction Dynamics Determine Signaling and Output Pathway Responses. Cell Rep 19(1):136-149
, 2017. A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants. Nat Commun 8(1):368
, 2017. Alternative transcriptional regulation in genome-reduced bacteria. Curr Opin Microbiol 39:89-95
, 2016. Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium. Cell Syst 2(6):391-401
, 2016. Bacterial antisense RNAs are mainly the product of transcriptional noise. Sci Adv 2(3):e1501363
, 2016. Cell type-specific properties and environment shape tissue specificity of cancer genes. Sci Rep 6:20707
, 2016. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Res 44(3):1192-202
, 2016. The yin-yang of kinase activation and unfolding explains the peculiarity of Val600 in the activation segment of BRAF. Elife 5:e12814
, 2016. Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome. Proteomics 16(4):554-63
, 2016. A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference. Elife 5.
, 2016. Decoy receptors block TRAIL sensitivity at a supracellular level: the role of stromal cells in controlling tumour TRAIL sensitivity. Oncogene 35(10):1261-70
, 2015. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Res 43(7):3465-77
, 2015. MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. Nucleic Acids Res 43(Database issue):D618-23
, 2015. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol Syst Biol 11(1):780
, 2015. Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae. Nucleic Acids Res 43(7):3442-53
, 2015. Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. Front Genet 6:260
, 2015. Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PLoS Comput Biol 11(5):e1004256
, 2015. Evolution of the SH3 Domain Specificity Landscape in Yeasts. PLoS One 10(6):e0129229
, 2015. Tuneable endogenous mammalian target complementation via multiplexed plasmid-based recombineering. Sci Rep 5:17432
, 2015. Comparative "-omics" in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors. PLoS One 10(9):e0137354
, 2014. Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations. Mol Syst Biol 10(5):727
, 2014. Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. J Proteome Res 13(1):300-13
, 2014. Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations. Biochim Biophys Acta 1844(9):1530-40
, 2014. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways. PLoS Comput Biol 10(6):e1003659
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, 2014. TAPAS: tools to assist the targeted protein quantification of human alternative splice variants. Bioinformatics 30(20):2989-90
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, 2013. In situ overlap and sequence synthesis during DNA assembly. ACS Synth Biol 2(12):750-5
, 2013. Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae. Mol Biosyst 9(7):1743-55
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, 2013. Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. Mol Syst Biol 9:653
, 2013. Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet 9(1):e1003191
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, 2012. SAPIN: a framework for the structural analysis of protein interaction networks. Bioinformatics 28(22):2998-9
, 2012. Structural data in synthetic biology approaches for studying general design principles of cellular signaling networks. Structure 20(11):1806-13
, 2011. Structural and functional protein network analyses predict novel signaling functions for rhodopsin. Mol Syst Biol 7:551
, 2011. Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol 9(9):658-69
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, 2008. DR4-selective tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) variants obtained by structure-based design. J Biol Chem 283(29):20560-8
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Publication list retrieved from NCBI using ImpactPubs
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