TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells von Li, Taiwen, Fan, Jingyu, Wang, Binbin, Traugh, Nicole, Chen, Qianming, Liu, Jun S, Li, Bo, Liu, X Shirley

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ON CONSISTENCY AND SPARSITY FOR SLICED INVERSE REGRESSION IN HIGH DIMENSIONS von Lin, Qian, Zhao, Zhigen, Liu, Jun S.

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Sequence determinants of improved CRISPR sgRNA design von Xu, Han, Xiao, Tengfei, Chen, Chen-Hao, Li, Wei, Meyer, Clifford A, Wu, Qiu, Wu, Di, Cong, Le, Zhang, Feng, Liu, Jun S, Brown, Myles, Liu, X Shirley

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Bayesian inference of epistatic interactions in case-control studies von Liu, Jun S, Zhang, Yu

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Topological domains in mammalian genomes identified by analysis of chromatin interactions von Dixon, Jesse R., Selvaraj, Siddarth, Yue, Feng, Kim, Audrey, Li, Yan, Shen, Yin, Hu, Ming, Liu, Jun S., Ren, Bing

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Convergent regulatory evolution and loss of flight in paleognathous birds von Sackton, Timothy B, Grayson, Phil, Cloutier, Alison, Hu, Zhirui, Liu, Jun S, Wheeler, Nicole E, Gardner, Paul P, Clarke, Julia A, Baker, Allan J, Clamp, Michele, Edwards, Scott V

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GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data von JIANXING FENG, MEYER, Clififord A, QIAN WANG, LIU, Jun S, SHIRLEY LIU, X, YONG ZHANG

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Bayesian inference of spatial organizations of chromosomes von Hu, Ming, Deng, Ke, Qin, Zhaohui, Dixon, Jesse, Selvaraj, Siddarth, Fang, Jennifer, Ren, Bing, Liu, Jun S

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Landscape of B cell immunity and related immune evasion in human cancers von Hu, Xihao, Zhang, Jian, Wang, Jin, Fu, Jingxin, Li, Taiwen, Zheng, Xiaoqi, Wang, Binbin, Gu, Shengqing, Jiang, Peng, Fan, Jingyu, Ying, Xiaomin, Zhang, Jing, Carroll, Michael C., Wucherpfennig, Kai W., Hacohen, Nir, Zhang, Fan, Zhang, Peng, Liu, Jun S., Li, Bo, Liu, X. Shirley

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Inference of transcriptional regulation in cancers von Jiang, Peng, Matthew L. Freedman, Jun S. Liu, Xiaole Shirley Liu

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HiCNorm: removing biases in Hi-C data via Poisson regression von MING HU, KE DENG, SELVARAJ, Siddarth, ZHAOHUI QIN, BING REN, LIU, Jun S

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MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens von Li, Wei, Xu, Han, Xiao, Tengfei, Cong, Le, Love, Michael I, Zhang, Feng, Irizarry, Rafael A, Liu, Jun S, Brown, Myles, Liu, X Shirley

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Revisit linear regression-based deconvolution methods for tumor gene expression data von Li, Bo, Liu, Jun S, Liu, X Shirley

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Partitioning and aggregating cross-tissue and tissue-specific genetic effects to identify gene-trait associations von Song, Shuang, Wang, Lijun, Hou, Lin, Liu, Jun S.

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Expansion of Biological Pathways Based on Evolutionary Inference von Li, Yang, Calvo, Sarah E., Gutman, Roee, Liu, Jun S., Mootha, Vamsi K.

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Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model von Sun, Xiaoxiao, Dalpiaz, David, Wu, Di, S Liu, Jun, Zhong, Wenxuan, Ma, Ping

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A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution von Gemmell, Patrick, Sackton, Timothy B, Edwards, Scott V, Liu, Jun S

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Determinants of transcription factor regulatory range von Chen, Chen-Hao, Zheng, Rongbin, Tokheim, Collin, Dong, Xin, Fan, Jingyu, Wan, Changxin, Tang, Qin, Brown, Myles, Liu, Jun S., Meyer, Clifford A., Liu, X. Shirley

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Bayesian biclustering of gene expression data von Gu, Jiajun, Liu, Jun S

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MetaGen: reference-free learning with multiple metagenomic samples von Xing, Xin, Liu, Jun S, Zhong, Wenxuan

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