How to Cite KINC¶

If you find KINC useful and would like to cite it please consider the following:

The following paper introduces the GMM approach as implemented in KINC for condition-specific modeling:

Sherman BT, Burns J, Feltus FA, Smith M, Ficklin SP. GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks (2019). IEEE Access. 7, 160845-160857

A second manuscript describing the full KINC pipeline for a Bioinformatic audience is currently in preparation. If you prefer to refer directly to the software itself please consider the following:

Josh Burns, Ben Shealy, Alex Feltus, Melissa Smith, & Stephen Ficklin. (2019, June 25). SystemsGenetics/KINC: Version 3.3.0 (Version v3.3.0). Zenodo. http://doi.org/10.5281/zenodo.3256358

Publications Using KINC¶

The following publications use KINC:

McKnight CB, Poulos AL, Bender MR, Calhoun JC, Feltus FA. Exploring Lossy Compression of Gene Expression Matrices (2019). IEEE/ACM 5th International Workshop on Data Analysis and Reduction for Big Scientific Data (DRBSD-5). 28-34
Shealey B, Burns JJR, Smith MC, Feltus FA, Ficklin SP. GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks (2019). IEEE Access. 7:160845-160857.
Poehlman WL, Schnabel E, Chavan S, Frugoli JA, Feltus FA. Identifying Temporally Regulated Root Nodulation Biomarkers Using Time Series Gene Co-Expression Network Analysis (2019). Frontiers in Plant Science. 10, p1409.
Honaas LA, Hargarten HL, Ficklin SP, Hadish JA, Wafula E, Mattheis JP, Rudell DR. Co-expression networks provide insights into molecular mechanisms of postharvest temperature modulation of apple fruit to reduce superficial scald (2019). Postharvest Biology and Technology, 149:27-41.
Dunwoodie LJ, Poehlman WL, Ficklin SP, Feltus FA. Discovery and validation of a glioblastoma co-expressed gene module (2018). Oncotarget. 9(13):10995–11008
Ficklin SP, Dunwoodie LJ, Poehlman WL, Watson C, Roche KE, Feltus FA. Discovering condition-specific gene co-expression patterns using gaussian mixture models: a cancer case study (2017) Scientific Reports. 7: 8617
Poehlman WL, Rynge M, Balamurugan D, Nills M, Feltus FA. OSG-KINC: High-throughput gene co-expression network construction using the open science grid (2017). IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1827-1831.