Correlation between gene expression profiles and protein-protein interactions within and across genomes. - Nitin Bhardwaj; Hui Lu 004 (Bioinform., 2005)

Improved protein fold assignment using support vector machines. - Robert E. Langlois; Alice Diec; Ognjen Perisic; Yang Dai; Hui Lu 004 (Int. J. Bioinform. Res. Appl., 2005)

MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins. - Nitin Bhardwaj; Robert V. Stahelin; Guijun Zhao; Wonhwa Cho; Hui Lu 004 (Bioinform., 2007)

Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP). - Zhi-Qiang Ye; Shuqi Zhao; Ge Gao; Xiao-Qiao Liu; Robert E. Langlois; Hui Lu 004; Liping Wei (Bioinform., 2007)

Co-Expression among Constituents of a Motif in the protein-protein Interaction Network. - Nitin Bhardwaj; Hui Lu 004 (J. Bioinform. Comput. Biol., 2009)

Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. - Nitin Bhardwaj; Mark Gerstein; Hui Lu 004 (BMC Bioinform., 2010)

An improved machine learning protocol for the identification of correct Sequest search results. - Morten Källberg; Hui Lu 004 (BMC Bioinform., 2010)

NAPS: a residue-level nucleic acid-binding prediction server. - Matthew B. Carson; Robert E. Langlois; Hui Lu 004 (Nucleic Acids Res., 2010)

Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets. - Nitin Bhardwaj; Matthew B. Carson; Alexej Abyzov; Koon-Kiu Yan; Hui Lu 004; Mark B. Gerstein (PLoS Comput. Biol., 2010)

A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains. - Morten Källberg; Nitin Bhardwaj; Robert E. Langlois; Hui Lu 004 (Bioinform., 2012)

Predicting essential genes for identifying potential drug targets in Aspergillus fumigatus. - Yao Lu; Jingyuan Deng; Judith C. Rhodes; Hui Lu 004; Long Jason Lu (Comput. Biol. Chem., 2014)

A novel essential domain perspective for exploring gene essentiality. - Yao Lu; Yulan Lu; Jingyuan Deng; Hai Peng; Hui Lu 004; Long Jason Lu (Bioinform., 2015)

A novel scoring estimator to screening for oncogenic chimeric transcripts in cancer transcriptome sequencing. - Jianlei Gu; Yao Lu; Shi-Yi Liu; Cong Liu 020; Hui Lu 004 (BIBM, 2016)

Implementation of a city-wide Health Information Exchange solution in the largest metropolitan region in China. - Guang-Jun Yu; Wenbin Cui; Li Zhou 007; David W. Bates; Jianlei Gu; Hui Lu 004 (BIBM, 2016)

High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI). - Cong Liu 020; Jianping Jiang; Jianlei Gu; Zhangsheng Yu; Tao Wang 067; Hui Lu 004 (BMC Syst. Biol., 2016)

Meta-analysis of sex differences in gene expression in schizophrenia. - Wenyi Qin; Cong Liu 020; Monsheel Sodhi; Hui Lu 004 (BMC Syst. Biol., 2016)

Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing. - Jianlei Gu; Yi-Zhong Wang; Shi-Yi Liu; Guang-Jun Yu; Ting Zhang; Hui Lu 004 (Neurocomputing, 2016)

Prediction of human QT prolongation liability based on pre-clinical RNA expression profiles. - Dennis M. Bergau; Cong Liu; Hui Lu 004 (BIBM, 2017)

A novel joint analysis framework improves identification of differentially expressed genes in cross disease transcriptomic analysis. - Wenyi Qin; Hui Lu 004 (BioData Min., 2018)

A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology. - Xiaofeng Gong; Jianping Jiang; Zhongqu Duan; Hui Lu 004 (BMC Bioinform., 2018)

CellSim: a novel software to calculate cell similarity and identify their co-regulation networks. - Leijie Li; Dongxue Che; Xiaodan Wang; Peng Zhang; Siddiq Ur Rahman; Jianbang Zhao; Jiantao Yu; Shiheng Tao; Hui Lu 004; Mingzhi Liao (BMC Bioinform., 2019)

Identifying and characterizing the effects of calendar and environmental conditions on pediatric admissions in Shanghai. - Guang-Jun Yu; Jianlei Gu; Wenbin Cui; Jianping Jiang; Yang Wang 079; Georgi Z. Genchev; Ting Lu; Hui Lu 004 (J. Big Data, 2019)

Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. - Sheng Yang; Hao Liu 081; Yangpeng Zhang; Hui Lu 004; Hai-Feng Chen (J. Chem. Inf. Model., 2019)

Predicting viral exposure response from modeling the changes of co-expression networks using time series gene expression data. - Fangli Dong; Yong He; Tao Wang 067; Dong Han; Hui Lu 004; Hongyu Zhao 003 (BMC Bioinform., 2020)

RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators. - Xujun Wang; Zhengtao Zhang; Wenyi Qin; Shiyi Liu; Cong Liu 020; Georgi Z. Genchev; Lijian Hui; Hongyu Zhao 003; Hui Lu 004 (Genom. Proteom. Bioinform., 2021)

MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys. - Tiantian Liu; Peirong Xu; Yueyao Du; Hui Lu 004; Hongyu Zhao 003; Tao Wang 067 (Briefings Bioinform., 2022)

A meta-learning approach to improving radiation response prediction in cancers. - Yuening Zhang; Li Qiu; Yongyong Ren; Zhiwei Cheng; Leijie Li; Siqiong Yao; Chengdong Zhang; Zhiguo Luo; Hui Lu 004 (Comput. Biol. Medicine, 2022)

scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data. - Fan Yang 081; Wenchuan Wang; Fang Wang 028; Yuan Fang; Duyu Tang; Junzhou Huang; Hui Lu 004; Jianhua Yao 001 (Nat. Mac. Intell., 2022)

Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective. - Jianlei Gu; Jiawei Dai; Hui Lu 004; Hongyu Zhao 003 (Genom. Proteom. Bioinform., 2023)

CARE as a wearable derived feature linking circadian amplitude to human cognitive functions. - Shuya Cui; Qingmin Lin; Yuanyuan Gui; Yunting Zhang; Hui Lu 004; Hongyu Zhao 003; Xiaolei Wang; Xinyue Li; Fan Jiang (npj Digit. Medicine, 2023)

HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol. - Zhiwei Cheng; Leijie Li; Yuening Zhang; Yongyong Ren; Jianlei Gu; Xinbo Wang; Hongyu Zhao 003; Hui Lu 004 (Briefings Bioinform., 2023)

diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype. - Daoyi Huang; Jianping Jiang; Tingting Zhao; Shengnan Wu; Pin Li; Yongfen Lyu; Jincai Feng; Mingyue Wei; Zhixing Zhu; Jianlei Gu; Yongyong Ren; Guangjun Yu; et al. (Bioinform., 2023)

Superresolved spatial transcriptomics transferred from a histological context. - Shu Wang; Xiaocheng Zhou; Yan Kong; Hui Lu 004 (Appl. Intell., 2023)

scGO: interpretable deep neural network for cell status annotation and disease diagnosis. - You Wu; Pengfei Xu; Liyuan Wang; Shuai Liu; Yingnan Hou; Hui Lu 004; Peng Hu; Xiaofei Li; Xiang Yu (Briefings Bioinform., 2024)

A sparse transformer generation network for brain imaging genetic association. - Hongrui Liu; Yuanyuan Gui; Hui Lu 004; Manhua Liu (Pattern Recognit., 2024)

Transformer with convolution and graph-node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image. - Xiao Xiao; Yan Kong; Ronghan Li; Zuoheng Wang; Hui Lu 004 (Medical Image Anal., 2024)

A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics. - Zhiwei Cheng; Yongyong Ren; Xinbo Wang; Yuening Zhang; Yingqi Hua; Hongyu Zhao 003; Hui Lu 004 (Briefings Bioinform., 2025)