Ralf Zimmer

The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.

Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.

How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.

Assessed papers (1)

• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.
  2023 L1 83/100

1 assessed by us (1 reproduced) · 256 not yet assessed — every PubMed paper on record, linked below.

• Divergent granulopoiesis at extramedullary sites safeguards antibacterial host defense ↗

  Science Immunology · 2026 · PMID 41996475
  not yet assessed
• Fuzzifier*: Robust and Sensitive Multi-omics Data Analysis ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2026
  not yet assessed
• Analysis and visualization of expression patterns with fuzzy sets as FlowSets ↗

  NAR Genomics and Bioinformatics · 2026 · PMID 42038406
  not yet assessed
• Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis and correlate with thrombus resolution ↗

  Immunity · 2025 · PMID 40280129
  not yet assessed
• Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2025
  not yet assessed
• Text Mining miRNA-gene Interactions for the mx-plore Platform ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• A molecular atlas of human granulopoiesis ↗

  Research Square · 2025
  not yet assessed
• ROQUIN-1 binding to the transcriptome of T cells reveals conserved targets in the control of lymphopoiesis ↗

  Research Square · 2025
  not yet assessed
• Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes ↗

  Nature Medicine · 2024 · PMID 38773340
  not yet assessed
• Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  eLife · 2024
  not yet assessed
• Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment ↗

  Science Advances · 2024 · PMID 38517968
  not yet assessed
• Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress ↗

  FEBS Letters · 2024 · PMID 38366111
  not yet assessed
• Augusta: From RNA‐Seq to gene regulatory networks and Boolean models ↗

  Computational and Structural Biotechnology Journal · 2024 · PMID 38312198
  not yet assessed
• Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  2024
  not yet assessed
• Author response: Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  2024
  not yet assessed
• Author Response: Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  2024
  not yet assessed
• Development of Novel Material Surfaces for Cardiovascular Implants Using Direct Laser Interference Patterning ↗

  The Thoracic and Cardiovascular Surgeon · 2024
  not yet assessed
• Reviewer #1 (Public Review): Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  2024
  not yet assessed
• Reviewer #2 (Public Review): Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  2024
  not yet assessed
• Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  eLife · 2024
  not yet assessed
• Author Response: Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  2024
  not yet assessed
• Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2024
  not yet assessed
• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation

  Immunity · 2023 · PMID 37652021
  L1 83/100
• Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  eLife · 2023 · PMID 38775664
  not yet assessed
• Multi-Omic Factor Analysis uncovers immunological signatures with pathophysiologic and clinical implications in coronary syndromes ↗

  medRxiv · 2023
  not yet assessed
• Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Detecting Differential Alternative Splicing in Mass Spectrometry-based Proteomics Data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia ↗

  eLife · 2023
  not yet assessed
• The Amino Acid Homoarginine Inhibits Atherogenesis by Modulating T-Cell Function ↗

  Circulation Research · 2022 · PMID 36102188
  not yet assessed
• Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival ↗

  Molecular Systems Biology · 2022 · PMID 36479616
  not yet assessed
• Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection ↗

  Nature Communications · 2022 · PMID 35197461
  not yet assessed
• Human genetic defects in SRP19 and SRPRA cause severe congenital neutropenia with distinctive proteome changes ↗

  Blood · 2022 · PMID 36223592
  not yet assessed
• Collecting SARS-CoV-2 Encoded miRNAs via Text Mining ↗

  Lecture notes in computer science · 2022
  not yet assessed
• Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium ↗

  Lecture notes in computer science · 2022
  not yet assessed
• Self-sustaining IL-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19 ↗

  JCI Insight · 2021 · PMID 34403366
  not yet assessed
• iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations ↗

  Journal of Proteome Research · 2021 · PMID 34383492
  not yet assessed
• Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2021
  not yet assessed
• Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2021
  not yet assessed
• Integrative functional genomics decodes herpes simplex virus 1 ↗

  Nature Communications · 2020 · PMID 32341360
  not yet assessed
• Vascular neutrophilic inflammation and immunothrombosis distinguish severe COVID‐19 from influenza pneumonia ↗

  Journal of Thrombosis and Haemostasis · 2020 · PMID 33217134
  not yet assessed
• EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing ↗

  Computational and Structural Biotechnology Journal · 2020 · PMID 32612757
  not yet assessed
• Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome ↗

  UNC Libraries · 2020
  not yet assessed
• Toward a gold standard for benchmarking gene set enrichment analysis ↗

  Briefings in Bioinformatics · 2019 · PMID 32026945
  not yet assessed
• The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins ↗

  Cell Reports · 2019 · PMID 31875563
  not yet assessed
• CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes ↗

  Bioinformatics · 2019 · PMID 31392308
  not yet assessed
• MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins ↗

  Molecular & Cellular Proteomics · 2019 · PMID 31235637
  not yet assessed
• From command-line bioinformatics to bioGUI ↗

  PeerJ · 2019 · PMID 31772845
  not yet assessed
• A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Biotechnology for Biofuels · 2019 · PMID 31636702
  not yet assessed
• Using Context-Sensitive Text Mining to Identify miRNAs in Different Stages of Atherosclerosis ↗

  Thrombosis and Haemostasis · 2019 · PMID 31378854
  not yet assessed
• Comparison of six breast cancer classifiers using qPCR ↗

  Bioinformatics · 2019 · PMID 30759193
  not yet assessed
• Multi-Reference Spectral Library Yields Almost Complete Coverage of Heterogeneous LC-MS/MS Data Sets ↗

  Journal of Proteome Research · 2019 · PMID 30793903
  not yet assessed
• YESdb: integrative analysis of environmental stress in yeast ↗

  Database · 2019 · PMID 30821814
  not yet assessed
• Integrative functional genomics decodes herpes simplex virus 1 ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Towards a gold standard for benchmarking gene set enrichment analysis ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• MS-EmpiRe utilizes peptide-level noise distributions for ultra sensitive detection of differentially abundant proteins ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Machine Learning Unveils Proteotypic Mimicry in Genetically Defined SCN Variants ↗

  Blood · 2019
  not yet assessed
• MOESM12 of A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Figshare · 2019
  not yet assessed
• MOESM9 of A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Figshare · 2019
  not yet assessed
• MOESM11 of A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Figshare · 2019
  not yet assessed
• MOESM3 of A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Figshare · 2019
  not yet assessed
• MOESM10 of A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Figshare · 2019
  not yet assessed
• MOESM5 of A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Figshare · 2019
  not yet assessed
• MOESM4 of A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock ↗

  Figshare · 2019
  not yet assessed
• Improved Ribo-seq enables identification of cryptic translation events ↗

  Nature Methods · 2018 · PMID 29529017
  not yet assessed
• Dicer in Macrophages Prevents Atherosclerosis by Promoting Mitochondrial Oxidative Metabolism ↗

  Circulation · 2018 · PMID 29748186
  not yet assessed
• miR-103 promotes endothelial maladaptation by targeting lncWDR59 ↗

  Nature Communications · 2018 · PMID 29980665
  not yet assessed
• Widespread modulation of gene expression by copy number variation in skeletal muscle ↗

  Scientific Reports · 2018 · PMID 29362391
  not yet assessed
• Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection ↗

  Scientific Reports · 2018 · PMID 30367157
  not yet assessed
• Detection of network motifs using three-way ANOVA ↗

  PLoS ONE · 2018 · PMID 30080876
  not yet assessed
• P3783miR-147 deficiency in macrophages exacerbates atherosclerosis in mice ↗

  European Heart Journal · 2018
  not yet assessed
• From command-line bioinformatics to bioGUI ↗

  2018
  not yet assessed
• P25 MIR-103 PROMOTES ENDOTHELIAL MALADAPTATION AND ATHEROSCLEROSIS BY TARGETING LNCWDR59 ↗

  Cardiovascular Research · 2018
  not yet assessed
• EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells ↗

  PLoS Pathogens · 2017 · PMID 28968461
  not yet assessed
• Manananggal - a novel viewer for alternative splicing events ↗

  BMC Bioinformatics · 2017 · PMID 28222683
  not yet assessed
• RelExplain—integrating data and networks to explain biological processes ↗

  Bioinformatics · 2017 · PMID 28165113
  not yet assessed
• Bioinformatics advances biology and medicine by turning big data troves into knowledge ↗

  Informatik-Spektrum · 2017
  not yet assessed
• MiR-103 target lncWDR59 to affect endothelial proliferation balanced by Notch1 and Wnt signaling co-activation ↗

  Atherosclerosis · 2017
  not yet assessed
• Multi-reference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge ↗

  2017
  not yet assessed
• Additional file 1: of Manananggal - a novel viewer for alternative splicing events ↗

  Figshare · 2017
  not yet assessed
• Additional file 1: of Manananggal - a novel viewer for alternative splicing events ↗

  Figshare · 2017
  not yet assessed
• Resolving Lipid Mediators Maresin 1 and Resolvin D2 Prevent Atheroprogression in Mice ↗

  Circulation Research · 2016 · PMID 27531933
  not yet assessed
• Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis ↗

  BMC Bioinformatics · 2016 · PMID 26791995
  not yet assessed
• Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle ↗

  PLoS ONE · 2016 · PMID 27348523
  not yet assessed
• Cross-species Conservation of context-specific networks ↗

  BMC Systems Biology · 2016 · PMID 27531214
  not yet assessed
• Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data ↗

  PLoS ONE · 2016 · PMID 27723775
  not yet assessed
• Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins ↗

  Journal of Molecular Biology · 2016 · PMID 26953259
  not yet assessed
• Small interfering RNAs (siRNA) genome-scale screen data for investigating host factors (HFs) involved in Herpes Simplex Virus Type 1 Replication ↗

  University of Edinburgh · 2016
  not yet assessed
• Young Investigator Abstract Session - Vascular258Pro-atherogenic miR-103 inhibits endothelial proliferation by targeting lncWDR59259Circulating long-non coding RNA LIPCAR and left ventricular diastolic function in patients with uncomplicated type 2 diabetes mellitus260Circulating thrombospondin-1 inhibits coronary blood flow reserve in aging hearts through a CD-47-dependent decrease in NO in coronary arterioles261Endothelial cell adenosine deaminase acting on RNA-1 is critically involved in vascular development and homeostasis in vivo262Sympathetic transmission in perivascular adipose tissue function in health and obesity ↗

  Cardiovascular Research · 2016
  not yet assessed
• Additional file 4 of Bioconductorâ s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis ↗

  Figshare · 2016
  not yet assessed
• Additional file 3 of Bioconductorâ s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis ↗

  Figshare · 2016
  not yet assessed
• Additional file 2 of Bioconductorâ s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis ↗

  Figshare · 2016
  not yet assessed
• Additional file 1 of Bioconductorâ s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis ↗

  Figshare · 2016
  not yet assessed
• Additional file 1 of Bioconductorâ s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis ↗

  Figshare · 2016
  not yet assessed
• Widespread disruption of host transcription termination in HSV-1 infection ↗

  Nature Communications · 2015 · PMID 25989971
  not yet assessed
• ContextMap 2: fast and accurate context-based RNA-seq mapping ↗

  BMC Bioinformatics · 2015 · PMID 25928589
  not yet assessed
• p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses ↗

  Molecular & Cellular Proteomics · 2015 · PMID 26183718
  not yet assessed
• Alternative Splicing in Next Generation Sequencing Data of Saccharomyces cerevisiae ↗

  PLoS ONE · 2015 · PMID 26469855
  not yet assessed
• Addressing false discoveries in network inference ↗

  Bioinformatics · 2015 · PMID 25910697
  not yet assessed
• Count ratio model reveals bias affecting NGS fold changes ↗

  Nucleic Acids Research · 2015 · PMID 26160885
  not yet assessed
• Microrna biogenesis in macrophages regulates mitochondrial energy metabolism and prevents atherosclerosis – Presentation cancelled ↗

  Atherosclerosis · 2015
  not yet assessed
• A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference ↗

  PLoS ONE · 2014 · PMID 24901222
  not yet assessed
• To be, or not to be: konservierte eukaryotische Regulationsnetzwerke? ↗

  BIOspektrum · 2014
  not yet assessed
• Widespread context dependency of microRNA-mediated regulation ↗

  Genome Research · 2014 · PMID 24668909
  not yet assessed
• Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set ↗

  BMC Biotechnology · 2013 · PMID 23688045
  not yet assessed
• A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication ↗

  PLoS Pathogens · 2013 · PMID 23950709
  not yet assessed
• Inactivation of Intergenic Enhancers by EBNA3A Initiates and Maintains Polycomb Signatures across a Chromatin Domain Encoding CXCL10 and CXCL9 ↗

  PLoS Pathogens · 2013 · PMID 24068939
  not yet assessed
• PARma: identification of microRNA target sites in AGO-PAR-CLIP data ↗

  Genome biology · 2013 · PMID 23895117
  not yet assessed
• Comprehensive Analysis of Varicella-Zoster Virus Proteins Using a New Monoclonal Antibody Collection ↗

  Journal of Virology · 2013 · PMID 23596286
  not yet assessed
• A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae ↗

  Nucleic Acids Research · 2013 · PMID 23873954
  not yet assessed
• Mining RNA–Seq Data for Infections and Contaminations ↗

  PLoS ONE · 2013 · PMID 24019895
  not yet assessed
• A Turing test for artificial expression data ↗

  Bioinformatics · 2013 · PMID 23956305
  not yet assessed
• A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation ↗

  Lipids in Health and Disease · 2013 · PMID 23827056
  not yet assessed
• Complementing the Eukaryotic Protein Interactome ↗

  PLoS ONE · 2013 · PMID 23825550
  not yet assessed
• Role of 5-hydroxymethylcytosine during postnatal retinal development

  Investigative Ophthalmology & Visual Science · 2013
  not yet assessed
• Degradation of Cellular miR-27 by a Novel, Highly Abundant Viral Transcript Is Important for Efficient Virus Replication In Vivo ↗

  PLoS Pathogens · 2012 · PMID 22346748
  not yet assessed
• Inferring gene regulatory networks by ANOVA ↗

  Bioinformatics · 2012 · PMID 22467911
  not yet assessed
• Experiment and mathematical modeling of gene expression dynamics in a cell-free system ↗

  Integrative Biology · 2012 · PMID 22481223
  not yet assessed
• Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection ↗

  PLoS Pathogens · 2012 · PMID 22969428
  not yet assessed
• Rigorous assessment of gene set enrichment tests ↗

  Bioinformatics · 2012 · PMID 22492315
  not yet assessed
• A context-based approach to identify the most likely mapping for RNA-seq experiments ↗

  BMC Bioinformatics · 2012 · PMID 22537048
  not yet assessed
• Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens ↗

  animal · 2012 · PMID 23228824
  not yet assessed
• RIP-chip enrichment analysis ↗

  Bioinformatics · 2012 · PMID 23104891
  not yet assessed
• Detection and correction of probe-level artefacts on microarrays ↗

  BMC Bioinformatics · 2012 · PMID 22647057
  not yet assessed
• Detecting outlier peptides in quantitative high-throughput mass spectrometry data ↗

  Journal of Proteomics · 2012 · PMID 22483996
  not yet assessed
• ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes ↗

  DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) · 2012
  not yet assessed
• 39 FACTORS INFLUENCING THE EFFICIENCY OF GENERATING GENETICALLY ENGINEERED PIGS BY NUCLEAR TRANSFER: MULTI-FACTORIAL ANALYSIS OF A LARGE DATA SET ↗

  Reproduction Fertility and Development · 2012
  not yet assessed
• Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution ↗

  Genome Research · 2012 · PMID 22539649
  not yet assessed
• The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors ↗

  PLoS Pathogens · 2011 · PMID 22046132
  not yet assessed
• From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems ↗

  Bioinformatics · 2011 · PMID 21685094
  not yet assessed
• MIRTFnet: Analysis of miRNA Regulated Transcription Factors ↗

  PLoS ONE · 2011 · PMID 21857930
  not yet assessed
• Contextual analysis of RNAi-based functional screens using interaction networks ↗

  Bioinformatics · 2011 · PMID 21835772
  not yet assessed
• The SARS-coronavirus-host interactome ↗

  Open access LMU (Ludwid Maxmilian's Universitat Munchen) · 2011
  not yet assessed
• Experiment Specific Expression Patterns ↗

  Lecture notes in computer science · 2011
  not yet assessed
• Experiment Specific Expression Patterns ↗

  Journal of Computational Biology · 2011 · PMID 21919744
  not yet assessed
• Systematic Analysis of Viral and Cellular MicroRNA Targets in Cells Latently Infected with Human γ-Herpesviruses by RISC Immunoprecipitation Assay ↗

  Cell Host & Microbe · 2010 · PMID 20413099
  not yet assessed
• Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer ↗

  Nucleic Acids Research · 2010 · PMID 20478826
  not yet assessed
• miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature ↗

  BMC Bioinformatics · 2010 · PMID 20233441
  not yet assessed
• Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization ↗

  PLoS ONE · 2010 · PMID 20862218
  not yet assessed
• Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis ↗

  PLoS Computational Biology · 2010 · PMID 20543878
  not yet assessed
• Classification of ncRNAs using position and size information in deep sequencing data ↗

  Bioinformatics · 2010 · PMID 20823303
  not yet assessed
• HALO—a Java framework for precise transcript half-life determination ↗

  Bioinformatics · 2010 · PMID 20299326
  not yet assessed
• Fuzzy Modeling ↗

  Computational biology · 2010
  not yet assessed
• FERN – Stochastic Simulation and Evaluation of Reaction Networks ↗

  Systems biology · 2010
  not yet assessed
• Vorescore—fold recognition improved by rescoring of protein structure models ↗

  Bioinformatics · 2010 · PMID 20823310
  not yet assessed
• CCDC 720141: Experimental Crystal Structure Determination ↗

  The Cambridge Structural Database · 2010
  not yet assessed
• Conserved principles of mammalian transcriptional regulation revealed by RNA half-life ↗

  Nucleic Acids Research · 2009 · PMID 19561200
  not yet assessed
• Evolutionarily Conserved Herpesviral Protein Interaction Networks ↗

  PLoS Pathogens · 2009 · PMID 19730696
  not yet assessed
• Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast ↗

  Journal of Computational Biology · 2009 · PMID 19630542
  not yet assessed
• Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis ↗

  BMC Structural Biology · 2009 · PMID 19374763
  not yet assessed
• Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum ↗

  PLoS Computational Biology · 2009 · PMID 19401785
  not yet assessed
• Transcript-Specific Expression Profiles Derived from Sequence-Based Analysis of Standard Microarrays ↗

  PLoS ONE · 2009 · PMID 19277110
  not yet assessed
• Identifying the topology of protein complexes from affinity purification assays ↗

  Bioinformatics · 2009 · PMID 19505940
  not yet assessed
• Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen ↗

  Informatik-Spektrum · 2009
  not yet assessed
• Evolution and divergence of herpesviral protein interaction networks

  2009
  not yet assessed
• High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay ↗

  RNA · 2008 · PMID 18658122
  not yet assessed
• Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast ↗

  Lecture notes in computer science · 2008
  not yet assessed
• ProCope—protein complex prediction and evaluation ↗

  Bioinformatics · 2008 · PMID 18635566
  not yet assessed
• Protein structure alignment considering phenotypic plasticity ↗

  Bioinformatics · 2008 · PMID 18689847
  not yet assessed
• Normalization strategies for mRNA expression data in cartilage research ↗

  Osteoarthritis and Cartilage · 2008 · PMID 18258458
  not yet assessed
• Normalization and Gene p-Value Estimation: Issues in Microarray Data Processing ↗

  Bioinformatics and Biology Insights · 2008 · PMID 19812783
  not yet assessed
• FERN – a Java framework for stochastic simulation and evaluation of reaction networks ↗

  BMC Bioinformatics · 2008 · PMID 18755046
  not yet assessed
• Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic.

  2008
  not yet assessed
• Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes ↗

  Bioinformatics · 2008 · PMID 18381403
  not yet assessed
• Identifying the Topology of Protein Complexes from Affinity Purification Assays.

  2008
  not yet assessed
• Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. ↗

  GI Jahrestagung (2) · 2008
  not yet assessed
• Erratum ↗

  Cytogenetics and Cell Genetics · 2008
  not yet assessed
• Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome ↗

  PLoS ONE · 2007 · PMID 17520018
  not yet assessed
• Alternative splicing and protein structure evolution ↗

  Nucleic Acids Research · 2007 · PMID 18055499
  not yet assessed
• Reconstruction, modeling &amp; analysis of <i>Halobacterium</i> <i>salinarum</i> R-1metabolism ↗

  Molecular BioSystems · 2007 · PMID 18213408
  not yet assessed
• BioWeka—extending the Weka framework for bioinformatics ↗

  Bioinformatics · 2007 · PMID 17237069
  not yet assessed
• Microarray analyses of transdifferentiated mesenchymal stem cells ↗

  Journal of Cellular Biochemistry · 2007 · PMID 17610236
  not yet assessed
• Vorolign—fast structural alignment using Voronoi contacts ↗

  Bioinformatics · 2007 · PMID 17237093
  not yet assessed
• Influence of degree correlations on network structure and stability in protein-protein interaction networks ↗

  BMC Bioinformatics · 2007 · PMID 17688687
  not yet assessed
• ProSAS: a database for analyzing alternative splicing in the context of protein structures ↗

  Nucleic Acids Research · 2007 · PMID 17933774
  not yet assessed
• AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings ↗

  Bioinformatics · 2007 · PMID 17379694
  not yet assessed
• Functional genomics, evo-devo and systems biology: a chance to overcome complexity? ↗

  Current Opinion in Rheumatology · 2007 · PMID 17762612
  not yet assessed
• AutoPSI: a database for automatic structural classification of protein sequences and structures ↗

  Nucleic Acids Research · 2007 · PMID 17932066
  not yet assessed
• Unsupervised Decision Trees Structured by Gene Ontology (GO-UDTs) for the Interpretation of Microarray Data ↗

  Studies in classification, data analysis, and knowledge organization · 2007
  not yet assessed
• Microarray analyses and bioinformatic evaluation of the plasticity between human mesenchymal stem cell-derived osteoblasts and adipocytes. ↗

  PubMed · 2007 · PMID 24692966
  not yet assessed
• Skeletal Rearrangement Reactions ↗

  Ene-X Compounds (X=S, Se, Te, N, P) · 2007
  not yet assessed
• Acknowledgments ↗

  Elsevier eBooks · 2007
  not yet assessed
• CCDC 601760: Experimental Crystal Structure Determination ↗

  The Cambridge Structural Database · 2007
  not yet assessed
• RelEx—Relation extraction using dependency parse trees ↗

  Bioinformatics · 2006 · PMID 17142812
  not yet assessed
• Large‐scale gene expression profiling reveals major pathogenetic pathways of cartilage degeneration in osteoarthritis ↗

  Arthritis & Rheumatism · 2006 · PMID 17075858
  not yet assessed
• Reliable gene signatures for microarray classification: assessment of stability and performance ↗

  Bioinformatics · 2006 · PMID 16882647
  not yet assessed
• Gene and protein nomenclature in public databases ↗

  BMC Bioinformatics · 2006 · PMID 16899134
  not yet assessed
• Inferring topology from clustering coefficients in protein-protein interaction networks ↗

  BMC Bioinformatics · 2006 · PMID 17137490
  not yet assessed
• Toward the complete interactome ↗

  Nature Biotechnology · 2006 · PMID 16763580
  not yet assessed
• IL-1β, but not BMP-7 leads to a dramatic change in the gene expression pattern of human adult articular chondrocytes—Portraying the gene expression pattern in two donors ↗

  Cytokine · 2006 · PMID 17161615
  not yet assessed
• Factors Influencing the Design of Mobile Services ↗

  Kluwer Academic Publishers eBooks · 2006
  not yet assessed
• Characterization of protein interactions

  2006
  not yet assessed
• 5 EVALUATION AND VALIDATION OF MICROARRAY DATA IN OSTEOARTHRITIS AND CARTILAGE RESEARCH ↗

  Osteoarthritis and Cartilage · 2006
  not yet assessed
• ProMiner: rule-based protein and gene entity recognition ↗

  BMC Bioinformatics · 2005 · PMID 15960826
  not yet assessed
• Comparison of the chondrosarcoma cell line SW1353 with primary human adult articular chondrocytes with regard to their gene expression profile and reactivity to IL-1β ↗

  Osteoarthritis and Cartilage · 2005 · PMID 15950496
  not yet assessed
• Colored Petri net modeling and simulation of signal transduction pathways ↗

  Metabolic Engineering · 2005 · PMID 16376130
  not yet assessed
• Gene expression profiling of serum- and interleukin-1β-stimulated primary human adult articular chondrocytes – A molecular analysis based on chondrocytes isolated from one donor ↗

  Cytokine · 2005 · PMID 15955710
  not yet assessed
• SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles ↗

  Bioinformatics · 2005 · PMID 16267083
  not yet assessed
• A simple approach for protein name identification: prospects and limits ↗

  BMC Bioinformatics · 2005 · PMID 15960827
  not yet assessed
• Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts ↗

  Bioinformatics · 2005 · PMID 16204115
  not yet assessed
• Identifying active transcription factors and kinases from expression data using pathway queries ↗

  Bioinformatics · 2005 · PMID 16204089
  not yet assessed
• Data processing effects on the interpretation of microarray gene expression experiments

  2005
  not yet assessed
• QUASAR—scoring and ranking of sequence–structure alignments ↗

  Bioinformatics · 2005 · PMID 16216828
  not yet assessed
• Probabilistic methods for predicting protein functions in protein-protein interaction networks ↗

  arXiv (Cornell University) · 2005
  not yet assessed
• Web servicing the biological office ↗

  Bioinformatics · 2005 · PMID 16204117
  not yet assessed
• New methods for joint analysis of biological networks and expression data ↗

  Bioinformatics · 2004 · PMID 15231545
  not yet assessed
• Arby: automatic protein structure prediction using profile–profile alignment and confidence measures ↗

  Bioinformatics · 2004 · PMID 15059818
  not yet assessed
• Analysis of Differential Gene Expression in Healthy and Osteoarthritic Cartilage and Isolated Chondrocytes by Microarray Analysis ↗

  Humana Press eBooks · 2004 · PMID 15280592
  not yet assessed
• Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses. ↗

  PubMed · 2004 · PMID 15480056
  not yet assessed
• Functional Genomics of Osteoarthritis ↗

  Clinical Orthopaedics and Related Research · 2004
  not yet assessed
• Knowledge representation model for systems-level analysis of signal transduction networks. ↗

  PubMed · 2004 · PMID 15706509
  not yet assessed
• ToPNet—an application for interactive analysis of expression data and biological networks ↗

  Bioinformatics · 2004 · PMID 14962941
  not yet assessed
• The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources ↗

  Bioinformatics · 2004 · PMID 14734319
  not yet assessed
• ProMiner: Organism-specific protein name detection using approximate string matching

  Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft) · 2004
  not yet assessed
• Combining secondary structure element alignment and profile-profile alignment for fold recognition

  2004
  not yet assessed
• Functional genomics of osteoarthritis — Evaluation of disease hypotheses ↗

  Pathology - Research and Practice · 2004
  not yet assessed
• GENE EXPRESSION IN CHONDROCYTES ASSESSED WITH USE OF MICROARRAYS ↗

  Journal of Bone and Joint Surgery · 2003 · PMID 12721354
  not yet assessed
• Microarrays: How Many Do You Need? ↗

  Journal of Computational Biology · 2003 · PMID 12935350
  not yet assessed
• New methods for joint analysis of biological networks and expression data.

  German Conference on Bioinformatics · 2003
  not yet assessed
• The promise and limitations of DNA microarray analysis: Comment on the editorial by Firestein and Pisetsky ↗

  Arthritis & Rheumatism · 2003 · PMID 12632449
  not yet assessed
• Cell biology and functional genomics of osteoarthritic chondrocytes ↗

  Arthritis Research · 2003
  not yet assessed
• Co-clustering of biological networks and gene expression data ↗

  Bioinformatics · 2002 · PMID 12169542
  not yet assessed
• PLAYING BIOLOGY'S NAME GAME: IDENTIFYING PROTEIN NAMES IN SCIENTIFIC TEXT ↗

  2002 · PMID 12603045
  not yet assessed
• PROFILE-PROFILE ALIGNMENT: A POWERFUL TOOL FOR PROTEIN STRUCTURE PREDICTION ↗

  2002 · PMID 12603033
  not yet assessed
• Functional genomics of osteoarthritis ↗

  Pharmacogenomics · 2002 · PMID 12223049
  not yet assessed
• Confidence measures for protein fold recognition ↗

  Bioinformatics · 2002 · PMID 12075015
  not yet assessed
• Microarrays ↗

  2002
  not yet assessed
• A hypergraph-based method for unification of existing protein structure- and sequence-families. ↗

  PubMed · 2002 · PMID 12542418
  not yet assessed
• A New Method for the Fast Solution of Protein-3D-Structures, Combining Experiments and Bioinformatics ↗

  2002
  not yet assessed
• Genexpressionsprofilierung adulter humaner Chondrozyten mittels der cDNA-Array-Technologie ↗

  Zeitschrift für Rheumatologie · 2002
  not yet assessed
• ProML--the protein markup language for specification of protein sequences, structures and families. ↗

  PubMed · 2002 · PMID 12542416
  not yet assessed
• Improving fold recognition of protein threading by experimental distance constraints. ↗

  PubMed · 2002 · PMID 12542417
  not yet assessed
• Centralization: a new method for the normalization of gene expression data ↗

  Bioinformatics · 2001 · PMID 11473024
  not yet assessed
• Improving Profile-Profile Alignments via Log Average Scoring ↗

  Lecture notes in computer science · 2001
  not yet assessed
• Centralization: A biologically sensible method for the normalization of gene expression data

  Max Planck Institute for Plasma Physics · 2001
  not yet assessed
• Improving Fold Recognition of Protein Threading by Experimental Distance Constraints.

  2001
  not yet assessed
• Protein Structure Prediction ↗

  Methods and principles in medicinal chemistry · 2001
  not yet assessed
• Confidence Measures for Fold Recognition. ↗

  German Conference on Bioinformatics · 2001
  not yet assessed
• A new Method for Unification of Existing Protein Structure- and Sequence-Families.

  German Conference on Bioinformatics · 2001
  not yet assessed
• Pathway analysis in metabolic databases via differential metabolic display (DMD) ↗

  Bioinformatics · 2000 · PMID 11108705
  not yet assessed
• Analysis of gene expression data with pathway scores. ↗

  PubMed · 2000 · PMID 10977101
  not yet assessed
• A Simple Iterative Approach to Parameter Optimization ↗

  Journal of Computational Biology · 2000
  not yet assessed
• A simple iterative approach to parameter optimization ↗

  2000 · PMID 11108475
  not yet assessed
• CCDC 138014: Experimental Crystal Structure Determination ↗

  The Cambridge Structural Database · 2000
  not yet assessed
• Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology

  Intelligent Systems in Molecular Biology · 1999
  not yet assessed
• Protein threading by recursive dynamic programming 1 1Edited by J. Thornton ↗

  Journal of Molecular Biology · 1999 · PMID 10395828
  not yet assessed
• New scoring schemes for protein fold recognition based on Voronoi contacts. ↗

  Bioinformatics · 1998 · PMID 9614274
  not yet assessed
• APPLICATION OF PARAMETER OPTIMIZATION TO MOLECULAR COMPARISON PROBLEMS ↗

  1998 · PMID 10380221
  not yet assessed
• Fast and numerically stable parametric alignment of biosequences ↗

  1997
  not yet assessed
• Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. ↗

  PubMed · 1996 · PMID 9390223
  not yet assessed
• Fast protein fold recognition and accurate sequence-structure alignment ↗

  Lecture notes in computer science · 1996
  not yet assessed
• Recursive dynamic programming for adaptive sequence and structure alignment. ↗

  PubMed · 1995 · PMID 7584462
  not yet assessed
• [Research on intravenous fat intake]. ↗

  PubMed · 1961 · PMID 13748354
  not yet assessed