Convergent network effects along the axis of gene expression during prostate cancer progression
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Manica M, Polig R, Purandare M, Mathis R, Hagleitner C, Martínez M. FPGA Accelerated Analysis of Boolean Gene Regulatory Networks. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2020, 17: 2141-2147. PMID: 31494553, DOI: 10.1109/tcbb.2019.2936836.Peer-Reviewed Original ResearchConceptsQualitative models of gene regulatory networksModels of gene regulatory networksAdvanced high-throughput technologiesGene regulatory networksHigh-throughput technologiesComplex molecular networkBoolean modelRegulatory networksBiological insightsT-cell large granular lymphocytic leukemiaMolecular networksAttractor detectionField Programmable Gate ArrayLarge granular lymphocytic leukemiaSoftware simulation toolGranular lymphocytic leukemiaSimulation toolPerformance improvementReconfigurable integrated circuitsCOSIFER: a Python package for the consensus inference of molecular interaction networks
Manica M, Bunne C, Mathis R, Cadow J, Ahsen M, Stolovitzky G, Martínez M. COSIFER: a Python package for the consensus inference of molecular interaction networks. Bioinformatics 2020, 37: 2070-2072. PMID: 33241320, PMCID: PMC8337002, DOI: 10.1093/bioinformatics/btaa942.Peer-Reviewed Original ResearchConceptsAdvent of high-throughput technologiesNetwork inferenceMolecular interaction networksHigh-throughput dataHigh-throughput technologiesState-of-the-artSupplementary dataExpression dataInteraction networkPython source codeInference servicesState-of-the-art methodologiesWeb servicesSource codeMolecular networksWeb-based platformRegulatory apparatusBioinformaticsPython packageConsensus strategyNetworkRobust networkInference methodsInferenceIndividual methods