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Online Preprints

  • J. Ding*, J. Lugo-Martinez*, Y. Yuan* and Z. Bar-Joseph. Reconstructing SARS-CoV-2 response signaling and regulatory networks. (2020) Preprint version is available at here. (*Indicates equal contribution)

  • D. Ruiz-Perez*, J. Lugo-Martinez*, N. Bourguignon, K. Mathee, B. Lerner, Z. Bar-Joseph and G. Narasimhan. Dynamic Bayesian networks for integrating muti-omics time-series microbiome data. (2020) Preprint version is available at here. (*Indicates equal contribution)

Complete Publications List

  • V. Pejaver, J. Urresti, J. Lugo-Martinez, K.A. Pagel, G.N. Lin, H.J. Nam, M. Mort, D.N. Cooper, J. Sebat, L.M. Iakoucheva, S.D. Mooney and P. Radivojac. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nature Communications. (2020) 11(1):5918. [PDF].

  • J. Lugo-Martinez, D. Zeiberg, T. Gaudelet, N. Malod-Dognin, N. Przulj and P. Radivojac. Classification in biological networks with hypergraphlet kernels. Bioinformatics. (2020), in press. [here]

  • J. Lugo-Martinez, J. Dengjel, Z. Bar-Joseph and R.F. Murphy. Integration of heterogeneous experimental data improves global map of human protein complexes. In Proc. of the 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. (ACM-BCB 2019). [PDF]

  • J. Lugo-Martinez*, D. Ruiz-Perez*, G. Narasimhan and Z. Bar-Joseph. Dynamic interaction network inference from longitudinal microbiome data. Microbiome. (2019) 7(1):54. (*Indicates equal contribution). [PDF]

  • M. Yamada, J. Tang, J. Lugo-Martinez, E. Hodzic, R. Shrestha, A. Saha, H. Ouyang, D. Yin, H. Mamitsuka, C. Sahinalp, P. Radivojac, F. Menczer and Y. Chang. Ultra high-dimensional nonlinear feature selection for big biological data. IEEE Transactions on Knowledge and Data Engineering. (2018) 30(7):1352-1365. [PDF]

  • T. Gaudelet, N. Malod-Dognin, J. Lugo-Martinez, P. Radivojac and N. Przulj. Hypergraphlets give insight into multi-scale organization of molecular networks. The 6th International Conference on Complex Networks and Their Applications. (2017) 41-43. [PDF]

  • J. Lugo-Martinez, V. Pejaver, K.A. Pagel, S. Jain, M. Mort, D.N. Cooper, S.D. Mooney and P. Radivojac. The loss and gain of functional residues is a frequent mechanism of human genetic disease. PLoS Computational Biology. (2016) 12(8):e1005091. [PDF]

  • J.F. Denton, J. Lugo-Martinez, A.E. Tucker, D.R. Schrider, W.C. Warren and M.W. Hahn. Extensive error in the number of genes inferred from draft genome assemblies. PLoS Computational Biology. (2014) 10(12):e1003998. [PDF]

  • J. Lugo-Martinez and P. Radivojac. Generalized graphlet kernels for probabilistic inference in sparse graphs. Network Science. (2014) 2(2):254-276. [PDF]

  • J. Lugo-Martinez and P. Radivojac. Vertex classification in graphs. Biomedical Computation Review. (Summer 2013) [PDF]

  • M.V. Han, G.W.C. Thomas, J. Lugo-Martinez and M.W. Hahn. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Molecular Biology and Evolution. (2013) 30:1987-1997. [PDF]

  • G. Venkatesh, J. Sampson, N. Goulding, S. Garcia, S. Bryksin, J. Lugo-Martinez, S. Swanson and M. Taylor. Conservation cores: Reducing the energy of mature computations. In Proc. of the 15th International Conference on Architectural Support for Programming Languages and Operating Systems. (ASPLOS 2010) 38:205-218. [PDF]