Items where Subject is "gene network"

Paper

Ballouz, S., Pavlidis, P., Gillis, J. (October 2016) Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Res. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Ballouz, S., Weber, M., Pavlidis, P., Gillis, J. (February 2017) EGAD: ultra-fast functional analysis of gene networks. Bioinformatics, 33 (4). pp. 612-614. ISSN 1367-4803

Ballouz, Sara, Weber, Melanie, Pavlidis, Paul, Gillis, Jesse (May 2016) EGAD: Ultra-fast functional analysis of gene networks. BioRxiv. (Unpublished)

Conn, A., Chandrasekhar, A., Rongen, M. V., Leyser, O., Chory, J., Navlakha, S. (September 2019) Network trade-offs and homeostasis in Arabidopsis shoot architectures. PLoS Comput Biol, 15 (9). e1007325. ISSN 1553-734x (Public Dataset)

Elkin, Rena, Oh, Jung Hun, Dela Cruz, Filemon, Norton, Larry, Deasy, Joseph O, Kung, Andrew L, Tannenbaum, Allen R (January 2024) Dynamic network curvature analysis of gene expression reveals novel potential therapeutic targets in sarcoma. Scientific Reports, 14 (1). p. 488. ISSN 2045-2322 (Public Dataset)

Fishell, G., Kepecs, A. (July 2019) Interneuron Types as Attractors and Controllers. Annu Rev Neurosci. ISSN 0147-006x

Ghotra, Rohan, Lee, Nicholas Keone, Tripathy, Rohit, Koo, Peter K (July 2021) Designing Interpretable Convolution-Based Hybrid Networks for Genomics. bioRxiv. (Submitted)

Kitagawa, M., Jackson, D. (April 2019) Control of Meristem Size. Annu Rev Plant Biol, 70. pp. 269-291. ISSN 1543-5008

Lee, J., Shah, M., Ballouz, S., Crow, M., Gillis, J. (May 2020) CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Research. ISSN 0305-1048

Lu, Guang-An, Zhang, Jinning, Zhao, Yixin, Chen, Qingjian, Lin, Pei, Tang, Tian, Tang, Zhixiong, Wen, Haijun, Liufu, Zhongqi, Wu, Chung-I (January 2023) Canalization of Phenotypes-When the Transcriptome is Constantly but Weakly Perturbed. Molecular Biology and Evolution, 40 (1). msad005. ISSN 0737-4038

Navlakha, S., Bar-Joseph, Z. (November 2011) Algorithms in nature: the convergence of systems biology and computational thinking. Mol Syst Biol, 7. p. 546. ISSN 1744-4292

Navlakha, S., He, X., Faloutsos, C., Bar-Joseph, Z. (July 2014) Topological properties of robust biological and computational networks. J R Soc Interface, 11 (96). p. 20140283. ISSN 1742-5662

Patro, R., Sefer, E., Malin, J., Marçais, G., Navlakha, S., Kingsford, C. (September 2012) Parsimonious reconstruction of network evolution. Algorithms for Molecular Biology, 7 (25). (Public Dataset)

Simhal, Anish K, Maclachlan, Kylee H, Elkin, Rena, Zhu, Jiening, Norton, Larry, Deasy, Joseph O, Oh, Jung Hun, Usmani, Saad Z, Tannenbaum, Allen (November 2023) Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival. Blood Cancer Journal, 13 (1). p. 175. ISSN 2044-5385

Verleyen, W., Ballouz, S., Gillis, J. (April 2016) Positive and negative forms of replicability in gene network analysis. Bioinformatics, 32 (7). pp. 1065-73. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Xu, Xiaosa, Jackson, David (December 2022) Single-cell analysis opens a goldmine for plant functional studies. Current Opinion in Biotechnology, 79. p. 102858. ISSN 0958-1669

Zhang, R, Atwal, GS, Lim, WK (March 2021) Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. Patterns, 2 (3). p. 100211. ISSN 2666-3899