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Lu Cheng
Lu Cheng
Department of Computer Science, Aalto University, Finland
Verified email at aalto.fi - Homepage
Title
Cited by
Cited by
Year
Hierarchical and spatially explicit clustering of DNA sequences with BAPS software
L Cheng, TR Connor, J Sirén, DM Aanensen, J Corander
Molecular biology and evolution 30 (5), 1224-1228, 2013
5102013
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
A Jolma, T Kivioja, J Toivonen, L Cheng, G Wei, M Enge, M Taipale, ...
Genome research 20 (6), 861-873, 2010
4612010
Dense genomic sampling identifies highways of pneumococcal recombination
C Chewapreecha, SR Harris, NJ Croucher, C Turner, P Marttinen, ...
Nature genetics 46 (3), 305-309, 2014
3632014
Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains
F Lebreton, W van Schaik, A Manson McGuire, P Godfrey, A Griggs, ...
MBio 4 (4), e00534-13, 2013
3482013
Cryptic ecology among host generalist Campylobacter jejuni in domestic animals
SK Sheppard, L Cheng, G Méric, CPA De Haan, AK Llarena, P Marttinen, ...
Molecular ecology 23 (10), 2442-2451, 2014
1262014
High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus
J Corander, KK Majander, L Cheng, J Merilä
Molecular ecology 22 (11), 2931–2940, 2013
1232013
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
SK Sieberts, F Zhu, J García-García, E Stahl, A Pratap, G Pandey, ...
Nature communications 7, 2016
892016
Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium
M de Been, W van Schaik, L Cheng, J Corander, RJ Willems
Genome biology and evolution 5 (8), 1524-1535, 2013
802013
An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data
L Cheng, S Ramchandran, T Vatanen, N Lietzén, R Lahesmaa, A Vehtari, ...
Nature communications 10 (1), 1-11, 2019
652019
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response
J Lin, C Tang, H Wei, B Du, C Chen, M Wang, Y Zhou, M Yu, L Cheng, ...
Cell host & microbe 29 (3), 489-502. e8, 2021
612021
The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome
A McNally, L Cheng, SR Harris, J Corander
Genome biology and evolution 5 (4), 699-710, 2013
612013
Estimating the transmission dynamics of Streptococcus pneumoniae from strain prevalence data
E Numminen, L Cheng, M Gyllenberg, J Corander
Biometrics 69 (3), 748-757, 2013
522013
Bayesian estimation of bacterial community composition from 454 sequencing data
L Cheng, AW Walker, J Corander
Nucleic acids research 40 (12), 5240-5249, 2012
352012
Random projection based clustering for population genomics
S Tasoulis, L Cheng, N Välimäki, NJ Croucher, SR Harris, WP Hanage, ...
2014 IEEE International Conference on Big Data (Big Data), 675-682, 2014
302014
Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model
V Jääskinen, V Parkkinen, L Cheng, J Corander
Statistical applications in genetics and molecular biology 13 (1), 105-121, 2014
232014
Bayesian semi-supervised classification of bacterial samples using MLST databases
L Cheng, TR Connor, DM Aanensen, BG Spratt, J Corander
BMC bioinformatics 12 (1), 1-10, 2011
232011
SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition
S Chatterjee, D Koslicki, S Dong, N Innocenti, L Cheng, Y Lan, ...
Bioinformatics 30 (17), 2423-2431, 2014
192014
Directional gene flow and ecological separation in Yersinia enterocolitica
S Reuter, J Corander, M de Been, S Harris, L Cheng, M Hall, ...
Microbial Genomics 1 (3), 2015
182015
Characterization and non-parametric modeling of the developing serum proteome during infancy and early childhood
N Lietzén, L Cheng, R Moulder, H Siljander, E Laajala, T Härkönen, ...
Scientific reports 8 (1), 1-13, 2018
102018
Profile of the oral microbiota from preconception to the third trimester of pregnancy and its association with oral hygiene practices
X La, H Jiang, A Chen, H Zheng, L Shen, W Chen, F Yang, L Zhang, X Cai, ...
Journal of oral microbiology 14 (1), 2053389, 2022
12022
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