Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data von Pratapa, Aditya, Jalihal, Amogh P., Law, Jeffrey N., Bharadwaj, Aditya, Murali, T. M.

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Hypergraph-based connectivity measures for signaling pathway topologies von Franzese, Nicholas, Groce, Adam, Murali, T M, Ritz, Anna

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The landscape of human proteins interacting with viruses and other pathogens von Dyer, Matthew D, Murali, T M, Sobral, Bruno W

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Comparative transcriptomic and phenotypic analysis of induced pluripotent stem cell hepatocyte-like cells and primary human hepatocytes von Gandhi, Neeti, Wills, Lauren, Akers, Kyle, Su, Yiqi, Niccum, Parker, Murali, T. M., Rajagopalan, Padmavathy

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Signaling hypergraphs von Ritz, Anna, Tegge, Allison N, Kim, Hyunju, Poirel, Christopher L, Murali, T.M

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The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis von Dyer, Matthew D, Neff, Chris, Dufford, Max, Rivera, Corban G, Shattuck, Donna, Bassaganya-Riera, Josep, Murali, T M, Sobral, Bruno W

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Computational prediction of host-pathogen protein–protein interactions von Dyer, Matthew D., Murali, T. M., Sobral, Bruno W.

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Supervised learning and prediction of physical interactions between human and HIV proteins von Dyer, Matthew D., Murali, T.M., Sobral, Bruno W.

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Whole-Genome Annotation by Using Evidence Integration in Functional-Linkage Networks von Karaoz, Ulas, Murali, T. M., Letovsky, Stan, Zheng, Yu, Ding, Chunming, Cantor, Charles R., Kasif, Simon

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Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin von Ruscio, Jory Z, Kumar, Deept, Shukla, Maulik, Prisant, Michael G, Murali, T.M, Onufriev, Alexey V

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The PathLinker app: Connect the dots in protein interaction networks [version 1; peer review: 1 approved, 2 approved with reservations] von Gil, Daniel P, Law, Jeffrey N, Murali, T. M

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RankGene: identification of diagnostic genes based on expression data von SU, Yang, MURALI, T. M, PAVLOVIC, Vladimir, SCHAFFER, Michael, KASIF, Simon

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Network-based prediction and analysis of HIV dependency factors von Murali, T M, Dyer, Matthew D, Badger, David, Tyler, Brett M, Katze, Michael G

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The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets von Kidane, Yared H, Lawrence, Christopher, Murali, T M

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Large-scale protein function prediction using heterogeneous ensembles [version 1; peer review: 2 approved] von Wang, Linhua, Law, Jeffrey, Kale, Shiv D, Murali, T. M, Pandey, Gaurav

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Pathways on demand: automated reconstruction of human signaling networks von Ritz, Anna, Poirel, Christopher L, Tegge, Allison N, Sharp, Nicholas, Simmons, Kelsey, Powell, Allison, Kale, Shiv D, Murali, TM

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Designing a Multicellular Organotypic 3D Liver Model with a Detachable, Nanoscale Polymeric Space of Disse von Larkin, Adam L., Rodrigues, Richard R., Murali, T.M., Rajagopalan, Padmavathy

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Automating the PathLinker app for Cytoscape von Huang, Li Jun, Law, Jeffrey N, Murali, T M

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Discovering networks of perturbed biological processes in hepatocyte cultures von Lasher, Christopher D, Rajagopalan, Padmavathy, Murali, T M

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Network-based functional enrichment von Poirel, Christopher L, Owens, 3rd, Clifford C, Murali, T M

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