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2020 – today
- 2021
[j11]Xu Shi
, Andrew F. Neuwald, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. Bioinform. 37(5): 650-658 (2021)- [j10]Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach. BMC Bioinform. 22(1): 193 (2021) - [j9]Xi Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements. PLoS Comput. Biol. 17(7) (2021)
2010 – 2019
- 2018
- [j8]Xu Shi, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data. Bioinform. 34(1): 56-63 (2018) - [j7]Xi Chen, Jinghua Gu, Xiao Wang, Jin-Gyoung Jung, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data. Bioinform. 34(10): 1733-1740 (2018) - 2017
- [j6]Xiao Wang, Jinghua Gu, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency. Bioinform. 33(2): 161-168 (2017) - [j5]Xi Chen, Xu Shi, Leena Hilakivi-Clarke, Ayesha N. Shajahan-Haq, Robert Clarke, Jianhua Xuan:
PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification. Bioinform. 33(2): 177-183 (2017) - 2015
- [j4]Xu Shi, Robert O. Barnes, Li Chen, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke, Yue Joseph Wang, Jianhua Xuan:
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. Bioinform. 31(14): 2412-2414 (2015) - 2014
- [j3]Jinghua Gu, Xiao Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data. BMC Bioinform. 15(S-9): S6 (2014) - [c5]Xi Chen, Xu Shi, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
Statistical Identification of Co-regulatory Gene Modules using Multiple ChIP-Seq Experiments. BIOINFORMATICS 2014: 109-116 - [c4]Xiao Wang, Jinghua Gu, Jianhua Xuan, Robert Clarke, Leena Hilakivi-Clarke:
A Markov random field-based Bayesian model to identify genes with differential methylation. CIBCB 2014: 1-8 - [c3]Xi Chen, Xu Shi, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data. EMBC 2014: 3937-3940 - 2013
- [j2]Xu Shi, Jinghua Gu, Xi Chen, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks. BMC Syst. Biol. 7(S-5): S4 (2013) - [c2]Jinghua Gu, Jianhua Xuan, Xiao Wang, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke:
Reconstructing transcriptional regulatory networks by probabilistic network component analysis. BCB 2013: 96 - [c1]Xi Chen, Jianhua Xuan, Xu Shi, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke:
A novel statistical approach to identify co-regulatory gene modules. BIBM 2013: 16-18 - 2011
- [j1]Bai Zhang, Ye Tian, Lu Jin, Huai Li, Ie-Ming Shih, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Leena Hilakivi-Clarke, Yue Joseph Wang:
DDN: a caBIG® analytical tool for differential network analysis. Bioinform. 27(7): 1036-1038 (2011)
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