Publication

Statistics and data analysis play important roles in all studies. All of our papers are open access or freely available online. If you have any problem, please contact. See Google Scholar for the full list.

Statistical Learning

NC Chung (2020) Statistical significance of cluster membership for unsupervised evaluation of cell identities. Bioinformatics; R Software

NC Chung, B Miasojedow, M Startek, A Gambin (2019) Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data. BMC bioinformatics; R Software

K Gogolewski*, M Sykulski*, NC Chung, A Gambin (2019) Truncated robust principal component analysis and noise reduction for single cell RNA sequencing data. Journal of Computational Biology; PDF

NC Chung, JD Storey (2015). Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics; R Software

Genomics

HJ Painter, NC Chung, A Sebastian, I Albert, JD Storey, M Llinás (2018). Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nature Communications; PlasmoDB; Figshare Data

NC Chung, J Szyda, M Frąszczak, 1000 Bull Genomes Project (2018). Population Structure Analysis of Bull Genomes of European and Western Ancestry. Scientific Reports

J Kim, N Ghasemzadeh, DJ Eapen, NC Chung, JD Storey, AA Quyyumi, G Gibson (2014). Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death. Genome Medicine; GEO Data

Proteomics

NC Chung, H Choi, D Wang, B Mirza, AR Pelletier, D Sigdel, W Wang, P Ping (2020) Identifying temporal molecular signatures underlying cardiovascular diseases; Journal of Molecular and Cellular Cardiology R Software

B Mirza, W Wang, J Wang, H Choi, NC Chung, P Ping (2019) Machine learning and integrative analysis of biomedical big data; Genes+

J Wang*, H Choi*, NC Chung, Q Cao, DCM Ng, B Mirza, SB Scruggs, D Wang, AO Garlid, P Ping (2018). Integrated dissection of the cysteine oxidative post-translational modification proteome during cardiac hypertrophy. Journal of Proteome Research; PDF; ProteomeXchange

Neural Networks

P Papadimitroulasa, L Brockic, NC Chung, W Marchadour, F Vermet, L Gaubert, V Eleftheriadis, D Plachouris, D Visvikis, GC Kagadis, M Hatt (2021). Deep learning in oncological radiomics and challenges of interpretability and data harmonization. Physica Medica; PDF

L Brocki, NC Chung (2019). Concept saliency maps to visualize relevant features in deep generative models. IEEE International Conference on Machine Learning and Applications (ICMLA); Code

NC Chung*, B Mirza*, H Choi, J Wang, D Wang, P Ping, W Wang (2019). Unsupervised classification of multi-omics data during cardiac remodeling using deep learning. Methods

Epidemiology

NC Chung, C Bolton-Moore, R Chilengi, MP Kasaro, JSA Stringer, BH Chi (2017) Patient engagement in HIV care and treatment in Zambia, 2004–2014; Tropical Medicine & International Health


* denote multiple first authors
+ denote review papers