Leena Hilakivi-Clarke

16 papers C 1Journal 11Unranked 4
YearRankTypeTitle / Venue / Authors
2021 J jnl
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach.
BMC Bioinform.
Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2021 J jnl
ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.
PLoS Comput. Biol.
Xi Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2021 J jnl
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles.
Bioinform.
Xu Shi, Andrew F. Neuwald, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2018 J jnl
CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data.
Bioinform.
Xi Chen, Jinghua Gu, Xiao Wang, Jin-Gyoung Jung, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2018 J jnl
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data.
Bioinform.
Xu Shi, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2017 J jnl
DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency.
Bioinform.
Xiao Wang, Jinghua Gu, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2017 J jnl
PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification.
Bioinform.
Xi Chen, Xu Shi, Leena Hilakivi-Clarke, Ayesha N. Shajahan-Haq, Robert Clarke, Jianhua Xuan
2015 J jnl
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.
Bioinform.
Xu Shi, Robert O. Barnes, Li Chen, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke, Yue Joseph Wang, Jianhua Xuan
2014 C conf
A Markov random field-based Bayesian model to identify genes with differential methylation.
CIBCB
Xiao Wang, Jinghua Gu, Jianhua Xuan, Robert Clarke, Leena Hilakivi-Clarke
2014 J jnl
BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data.
BMC Bioinform.
Jinghua Gu, Xiao Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2014 — conf
BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data.
EMBC
Xi Chen, Xu Shi, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2014 — conf
Statistical Identification of Co-regulatory Gene Modules using Multiple ChIP-Seq Experiments.
BIOINFORMATICS
Xi Chen, Xu Shi, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2013 — conf
A novel statistical approach to identify co-regulatory gene modules.
BIBM
Xi Chen, Jianhua Xuan, Xu Shi, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke
2013 — conf
Reconstructing transcriptional regulatory networks by probabilistic network component analysis.
BCB
Jinghua Gu, Jianhua Xuan, Xiao Wang, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke
2013 J jnl
mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks.
BMC Syst. Biol.
Xu Shi, Jinghua Gu, Xi Chen, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2011 J jnl
DDN: a caBIG
Bioinform.
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