Haiyan Hu

发表

Hierarchical order of gene expression levels

Haiyan Hu, X. Li, 2010, 2010 International Conference on Bioinformatics and Biomedical Technology.

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.).

Maojun Wang, Lili Tu, Pengcheng Wang, 2015, The New phytologist.

GhJAZ2 negatively regulates cotton fiber initiation by interacting with the R2R3-MYB transcription factor GhMYB25-like.

Lili Tu, Longfu Zhu, Xianlong Zhang, 2016, The Plant journal : for cell and molecular biology.

GhJAZ 2 negatively regulates cotton fiber initiation by interacting with the R 2 R 3-MYB transcription factor GhMYB 25-like

Lili Tu, Longfu Zhu, Xianlong Zhang, 2016 .

MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs

Jianfei Hu, Xiaoman Li, Haiyan Hu, 2008, Nucleic acids research.

Genetic Diversity, Population Structure, and Botanical Variety of 320 Global Peanut Accessions Revealed Through Tunable Genotyping-by-Sequencing

Feng Cheng, Haiyan Hu, Lei Shi, 2018, Scientific Reports.

Hundreds of motif pairs may facilitate enhancer-promoter interactions

Haiyan Hu, X. Li, Saidi Wang, 2020, bioRxiv.

An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments

Haiyan Hu, 2009, Bioinformatics and biology insights.

Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes.

Haiyan Hu, X. Li, Saidi Wang, 2020, Genomics.

Considering founding and variable genomes is critical in studying polyploid evolution

Yaxi Liu, Guoyue Chen, Yu-ming Wei, 2019, bioRxiv.

Bioinformatics Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar 1 [ C ] [ W ] [ OA ]

Jun Ding, Haiyan Hu, X. Li, 2011 .

SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data

Jun Ding, Haiyan Hu, X. Li, 2013, Nucleic acids research.

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics1[C][W]

Jun Ding, Haiyan Hu, X. Li, 2012, Plant Physiology.

Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus

Haiyan Hu, Xiaoman Shawn Li, Haiyan Hu, 2007, Pacific Symposium on Biocomputing.

Systematic discovery of cofactor motifs from ChIP-seq data by SIOMICS.

Jun Ding, Haiyan Hu, X. Li, 2015, Methods.

Long non-coding RNAs and their proposed functions in fibre 1 development of cotton ( Gossypium spp . ) 2 3

Maojun Wang, Lili Tu, Pengcheng Wang, 2016 .

INSISTC: Incorporating Network Structure Information for Single-Cell Type Classification

Haiyan Hu, X. Li, Saidi Wang, 2022, bioRxiv.

A new measurement of sequence conservation

Haiyan Hu, X. Li, Xiaohui Cai, 2009, BMC Genomics.

A revisit to universal single-copy genes in bacterial genomes

Haiyan Hu, X. Li, M. Ventolero, 2022, bioRxiv.

GhJAZ2 attenuates cotton resistance to biotic stresses via the inhibition of the transcriptional activity of GhbHLH171.

Longfu Zhu, Xianlong Zhang, Xin He, 2018, Molecular plant pathology.

Long non-coding RNAs and their proposed functions in fibre 1 development of cotton ( Gossypium spp.)

Maojun Wang, Lili Tu, Pengcheng Wang, 2020 .

Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins

H. Daniell, Jun Ding, Haiyan Hu, 2012, Plant Molecular Biology.

Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs

Haiyan Hu, X. Li, Yiyu Zheng, 2014, Nucleic acids research.

GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring.

Lili Tu, Daojun Yuan, Xianlong Zhang, 2016, Plant biotechnology journal.

Whole genome identification of target genes of transcription factors

Haiyan Hu, X. Li, 2010, 2010 International Conference on Bioinformatics and Biomedical Technology.

Precise epigenomic editing with a SunTag-based modular epigenetic toolkit

Haiyan Hu, Yoon-Seong Kim, S. Guhathakurta, 2022, Epigenetics.

Transcription Factor Binding Site Identification by Phylogenetic Footprinting

Haiyan Hu, X. Li, 2010 .

A systematic study of HIF1A cofactors in hypoxic cancer cells

Haiyan Hu, X. Li, Saidi Wang, 2022, bioRxiv.

Are known bacterial strains really present?

Haiyan Hu, X. Li, M. Ventolero, 2022, bioRxiv.

SMS: A Novel Approach for Bacterial Strain Genome Reconstruction in Multiple Samples

Haiyan Hu, X. Li, M. Ventolero, 2021 .

Systematic Prediction of Cis-Regulatory Elements in Chlamydomonas reinhardtii Genome Using Comparative Genomics

Jun Ding, Haiyan Hu, X. Li, 2012 .

An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid ‘Huaza Mian H318’, as revealed by genome-wide gene expression analysis

Maojun Wang, Yizan Ma, Longfu Zhu, 2020, BMC genomics.

Genes gained and lost during the evolution and domestication of Brassica napus

Yaxi Liu, Haiyan Hu, Wei Yuming, 2020 .

Chapter 6 Pattern Mining Across Many Massive Biological Networks

Juan Nunez-Iglesias, Xifeng Yan, Wenyuan Li, 2011 .

NIM, A Novel Computational Method for Predicting Nuclear-Encoded Chloroplast Proteins

Jun Ding, Haiyan Hu, X. Li, 2013 .

Silencing of glycerol-3-phosphate acyltransferase 6 (GPAT6) gene using a newly established virus induced gene silencing (VIGS) system in cucumber alleviates autotoxicity mimicked by cinnamic acid (CA)

Puwen Song, Haiyan Hu, Chengwei Li, 2019, Plant and Soil.

Isolation and characterization of a novel cyanophycin synthetase from a deep-sea sediment metagenomic library

Haiyan Hu, Yongjun Lu, Shining Zhou, 2013, Applied Microbiology and Biotechnology.

Computational discovery of feature patterns in nucleosomal DNA sequences.

Haiyan Hu, X. Li, Yiyu Zheng, 2014, Genomics.

MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects.

Haiyan Hu, X. Li, Ying Wang, 2016, Omics : a journal of integrative biology.

Low pH stress responsive transcriptome of seedling roots in wheat (Triticum aestivum L.)

Jie He, Haiyan Hu, X. Ou, 2018, Genes & Genomics.

Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins

H. Daniell, Jun Ding, Haiyan Hu, 2012, Plant Molecular Biology.

QTL mapping for grain number per spikelet in wheat using a high-density genetic map

Yu Lin, Yaxi Liu, Haiyan Hu, 2021 .

Low pH stress responsive transcriptome of seedling roots in wheat (Triticum aestivum L.)

Jie He, Haiyan Hu, X. Ou, 2018, Genes & Genomics.

A Novel QTL Conferring Fusarium Crown Rot Resistance Located on Chromosome Arm 6HL in Barley

Yaxi Liu, Meixue Zhou, Haiyan Hu, 2019, bioRxiv.

Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta)

Songnian Hu, Guangce Wang, Haiyan Hu, 2010 .

BHap: a novel approach for bacterial haplotype reconstruction

Xin Li, Haiyan Hu, Samaneh Saadat, 2019, Bioinform..

Mining coherent dense subgraphs across massive biological networks for functional discovery

Jiawei Han, Haiyan Hu, Xifeng Yan, 2005, ISMB.

A computational modeling of primary-microRNA expression

Haiyan Hu, X. Li, Saidi Wang, 2022, bioRxiv.

A two-stream convolutional neural network for microRNA transcription start site feature integration and identification

Haiyan Hu, X. Li, Hansi Zheng, 2021, Scientific Reports.

Computational annotation of miRNA transcription start sites

Xiaoman Li, Mingyu Cha, Haiyan Hu, 2020, Briefings Bioinform..

A systematic study of motif pairs that may facilitate enhancer–promoter interactions

Haiyan Hu, X. Li, Saidi Wang, 2022, J. Integr. Bioinform..

A Systematic Study of Motif Pairs That May Facilitate Enhancer-Promoter Interactions

Haiyan Hu, X. Li, Saidi Wang, 2021 .

Interpretation of deep learning in genomics and epigenomics

Clayton Barham, Xiaoman Li, Haiyan Hu, 2020, Briefings Bioinform..

Prognostic cancer gene signatures share common regulatory motifs

S. Goodison, Haiyan Hu, X. Li, 2017, Scientific Reports.

Position-wise binding preference is important for miRNA target site prediction

Xiaoman Li, Haiyan Hu, Amlan Talukder, 2020, Bioinform..

CCmiR: a computational approach for competitive and cooperative microRNA binding prediction

Jun Ding, Haiyan Hu, Xiaoman Li, 2018, Bioinform..

TarPmiR: a new approach for microRNA target site prediction

Jun Ding, Haiyan Hu, Xiaoman Li, 2016, Bioinform..

Discover the semantic structure of human reference epigenome by differential latent dirichlet allocation

Haiyan Hu, Xiaoman Li, Yiyu Zheng, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

ChIPModule: Systematic Discovery of Transcription Factors and Their Cofactors from ChIP-seq Data

Ying Wang, Jun Ding, Haiyan Hu, 2012, Pacific Symposium on Biocomputing.

When old metagenomic data meet newly sequenced genomes, a case study

Xin Li, Xiaoman Li, Haiyan Hu, 2018, PloS one.

An intriguing characteristic of enhancer-promoter interactions

Haiyan Hu, X. Li, Amlan Talukder, 2020, BMC Genomics.

PETModule: a motif module based approach for enhancer target gene prediction

Xiaoman Li, Haiyan Hu, Haiyan Hu, 2016, Scientific Reports.

Integrative analyses shed new light on human ribosomal protein gene regulation

Haiyan Hu, X. Li, Yiyu Zheng, 2016, Scientific Reports.

PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples

Haiyan Hu, Xiaoman Li, Yiyu Zheng, 2015, Database J. Biol. Databases Curation.

H3K4me2 reliably defines transcription factor binding regions in different cells.

Xiaoman Li, Ying Wang, Haiyan Hu, 2014, Genomics.

Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar1[C][W][OA]

Xiaoman Li, Haiyan Hu, Jun Ding, 2012, Plant Physiology.

Transcriptional regulation of co-expressed microRNA target genes.

Xiaoman Li, Ying Wang, Haiyan Hu, 2011, Genomics.

Systematic identification of conserved motif modules in the human genome

Minghua Deng, Lin Hou, Haiyan Hu, 2010, BMC Genomics.

An efficient algorithm to identify coordinately activated transcription factors.

Haiyan Hu, Haiyan Hu, 2010, Genomics.

A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference

Haiyan Hu, X. Li, James S Choi, 2022, bioRxiv.

mixtureS: a novel tool for bacterial strain genome reconstruction from reads

Xiaoman Li, Haiyan Hu, Xin Li, 2020, Bioinform..

Dynamic transcriptomes of human myeloid leukemia cells.

Songnian Hu, Jiangwei Yan, Xiangdong Fang, 2013, Genomics.

Repression of microRNA 160 results in retarded seed integument growth and smaller final seed size in cotton

Lili Tu, Zhonghua Li, Xianlong Zhang, 2020 .

Delineating a locus conferring Fusarium crown rot resistance on chromosome arm 1HL in barley by developing and analysing a large population derived from near isogenic lines

Meixue Zhou, Haiyan Hu, J. Stiller, 2020 .

Transcriptomic repertoires depict the initiation of lint and fuzz fibres in cotton (Gossypium hirsutum L.)

Maojun Wang, Lili Tu, Xianlong Zhang, 2017, Plant biotechnology journal.

GhH2A12, a replication-dependent histone H2A gene from Gossypium hirsutum, is negatively involved in the development of cotton fiber cells

Lili Tu, Xianlong Zhang, Haiyan Hu, 2014, Plant Cell Reports.

A Genetic and Metabolic Analysis Revealed that Cotton Fiber Cell Development Was Retarded by Flavonoid Naringenin1[W][OA]

Lili Tu, Xianlong Zhang, Haiyan Hu, 2013, Plant Physiology.

GbTCP, a cotton TCP transcription factor, confers fibre elongation and root hair development by a complex regulating system

Lili Tu, Xianlong Zhang, Haiyan Hu, 2012, Journal of experimental botany.

Genome-Wide Association Study of Kernel Traits in Aegilops tauschii

Yu Lin, Yaxi Liu, Haiyan Hu, 2021, Frontiers in Genetics.

Systematic discovery of functional modules and context-specific functional annotation of human genome

Haifeng Li, Haiyan Hu, Xifeng Yan, 2007, ISMB/ECCB.

MBBC: an efficient approach for metagenomic binning based on clustering

Ying Wang, Haiyan Hu, Xiaoman Li, 2015, BMC Bioinformatics.

Identification and functional analysis of the CorA/MGT/MRS2-type magnesium transporter in banana

Jiaquan Huang, Haiyan Hu, Wen Liu, 2020, PloS one.

The Chromosome-Level Genome of Miracle Fruit (Synsepalum dulcificum) Provides New Insights Into the Evolution and Function of Miraculin

Ping Li, Haiyan Hu, Zhenhua Liu, 2022, Frontiers in Plant Science.

A systematic evaluation of the computational tools for lncRNA identification

Haiyan Hu, X. Li, Hansi Zheng, 2021, Briefings Bioinform..

Transcriptional regulation in eukaryotic ribosomal protein genes.

Xiaoman Li, Haiyan Hu, Haiyan Hu, 2007, Genomics.

JunD/AP-1-Mediated Gene Expression Promotes Lymphocyte Growth Dependent on Interleukin-7 Signal Transduction

A. Khaled, Haiyan Hu, X. Li, 2012, PloS one.

Identification and Validation of a Novel Major Quantitative Trait Locus for Plant Height in Common Wheat (Triticum aestivum L.)

Yaxi Liu, Y. Tao, Haiyan Hu, 2020, Frontiers in Genetics.

Phenotypic and genetic variation in phosphorus-deficiency-tolerance traits in Chinese wheat landraces

Yaxi Liu, Haiyan Hu, Guang-deng Chen, 2020, BMC Plant Biology.

Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat.

Haiyan Hu, X. Ye, Chunji Liu, 2020, The New phytologist.

A deep learning method for miRNA/isomiR target detection

Haiyan Hu, X. Li, Wencai Zhang, 2022, Scientific Reports.

Homoploid hybridization signals due to ancestral subdivision: a case study on the D lineage in wheat

Haiyan Hu, X. Ye, Chunji Liu, 2019, bioRxiv.

Improving miRNA Target Prediction Using CLASH Data.

Haiyan Hu, Xiaoman Li, Haiyan Hu, 2019, Methods in molecular biology.

Isolation and characterization of a novel cyanophycin synthetase from a deep-sea sediment metagenomic library

Haiyan Hu, Yongjun Lu, Shining Zhou, 2013, Applied Microbiology and Biotechnology.

MicroRNA modules prefer to bind weak and unconventional target sites

Jun Ding, Haiyan Hu, Xiaoman Li, 2014, Bioinform..

Genetic Diversity, Population Structure, and Botanical Variety of 320 Global Peanut Accessions Revealed Through Tunable Genotyping-by-Sequencing

Feng Cheng, Haiyan Hu, Lei Shi, 2018, Scientific Reports.

Deep Learning to Identify Transcription Start Sites from CAGE Data

Haiyan Hu, Hansi Zheng, Xiaoman Li, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Application of Deep Learning Models to MicroRNA Transcription Start Site Identification

Clayton Barham, Xiaoman Li, Haiyan Hu, 2019, 2019 IEEE 7th International Conference on Bioinformatics and Computational Biology ( ICBCB).

Pattern Mining Across Many Massive Biological Networks

Haifeng Li, Xifeng Yan, Min Xu, 2012 .

Characterization of genes in guar gum biosynthesis based on quantitative RNA-sequencing in guar bean (Cyamopsis tetragonoloba)

Jiaquan Huang, Haiyan Hu, Yuanhao Ding, 2019, Scientific Reports.

MicroRNA 157-targeted SPL genes regulate floral organ size and ovule production in cotton

Lili Tu, Xianlong Zhang, Haiyan Hu, 2017, BMC Plant Biology.

Puwen Song, Haiyan Hu, Chengwei Li, 2019, Plant and Soil.

Systematic identification of conserved motif modules in the human genome

Minghua Deng, Lin Hou, Haiyan Hu, 2010, BMC Genomics.

FlexSLiM: a Novel Approach for Short Linear Motif Discovery in Protein Sequences

Ping Ge, Haiyan Hu, Xiaoman Li, 2018, ICBCB 2018.

Mining patterns in disease classification forests

Haiyan Hu, Haiyan Hu, 2010, J. Biomed. Informatics.

rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database

Ying Wang, Haiyan Hu, Xiaoman Li, 2017, J. Comput. Biol..

Multimodal deep learning approaches for single-cell multi-omics data integration

Haiyan Hu, X. Li, Tasbiraha Athaya, 2023, Briefings Bioinform..

Frequent Pattern Discovery in Multiple Biological Networks: Patterns and Algorithms

Xifeng Yan, Min Xu, Xianghong Jasmine Zhou, 2012 .

Frequent Pattern Discovery in Multiple Biological Networks: Patterns and Algorithms

Juan Nunez-Iglesias, Xifeng Yan, Wenyuan Li, 2011, Statistics in Biosciences.

Small RNA sequencing revealed various microRNAs involved in ethylene-triggered flowering process in Aechmea fasciata

Li Xu, Haiyan Hu, Jia-bin Wang, 2020, Scientific Reports.

Transcriptional regulation of co-expressed microRNA target genes.

Haiyan Hu, X. Li, Ying Wang, 2011, Genomics.

A Genetic and Metabolic Analysis Revealed that Cotton Fiber Cell Development Was Retarded by Flavonoid Naringenin1[W][OA]

Lili Tu, Xianlong Zhang, Haiyan Hu, 2013, Plant Physiology.

GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring.

Lili Tu, Daojun Yuan, Xianlong Zhang, 2015, Plant biotechnology journal.

EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction

Samaneh Saadat, Haiyan Hu, X. Li, 2019, Bioinform..

SMS: A Novel Approach for Bacterial Strain Analysis in Multiple Samples

Haiyan Hu, X. Li, Saidi Wang, 2023, Journal of Bioinformatics and Systems Biology.

Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids.

Yaxi Liu, Guoyue Chen, Haiyan Hu, 2021, Genome.

GhH2A12, a replication-dependent histone H2A gene from Gossypium hirsutum, is negatively involved in the development of cotton fiber cells

Lili Tu, Xianlong Zhang, Haiyan Hu, 2014, Plant Cell Reports.

Computational analyses of bacterial strains from shotgun reads

Haiyan Hu, X. Li, M. Ventolero, 2022, Briefings Bioinform..

Running head: Flavonoid Naringenin affected Fiber Development

Lili Tu, Xianlong Zhang, Haiyan Hu, 2013 .

A computational modeling of pri-miRNA expression

Haiyan Hu, X. Li, Saidi Wang, 2024, PloS one.

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics1[C][W]

Jun Ding, Haiyan Hu, X. Li, 2012, Plant Physiology.