Weiqiang Zhou

Research output

Research output per year 1999 2013 2021 2023 2024

• 41 Article
• 6 Conference contribution
• 3 Review article
• 1 Letter

Research output per year

Research output per year

Search results

• 2024

  Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children

  Andargie, T. E., Roznik, K., Redekar, N., Hill, T., Zhou, W., Apalara, Z., Kong, H., Gordon, O., Meda, R., Park, W., Johnston, T. S., Wang, Y., Brady, S., Ji, H., Yanovski, J. A., Jang, M. K., Lee, C. M., Karaba, A. H., Cox, A. L. & Agbor-Enoh, S., Jan 2 2024, In: The Journal of clinical investigation. 134, 1

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2023

  Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children

  Andargie, T. E., Roznik, K., Redekar, N., Hill, T., Zhou, W., Apalara, Z., Kong, H., Gordon, O., Meda, R., Park, W., Johnston, T. S., Wang, Y., Brady, S., Ji, H., Yanovski, J. A., Jang, M. K., Lee, C. M., Karaba, A. H., Cox, A. L. & Agbor-Enoh, S., Nov 1 2023, In: Journal of Clinical Investigation. 133, 21, e171729.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cell-Free Nucleic Acids 100%
  • Pathology 50%
  • Child 34%
  • Pediatrics 29%
  • Wounds and Injuries 16%

• DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence

  Fang, Y., Ji, Z., Zhou, W., Abante, J., Koldobskiy, M. A., Ji, H. & Feinberg, A. P., Mar 21 2023, In: Nucleic acids research. 51, 5, p. 2046-2065 20 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Entropy 100%
  • DNA Methylation 82%
  • Methylation 75%
  • Epigenomics 72%
  • Information Theory 31%

• Identification of Regulatory Elements in Primary Sensory Neurons Involved in Trauma-Induced Neuropathic Pain

  Stephens, K. E., Moore, C., Vinson, D. A., White, B. E., Renfro, Z., Zhou, W., Ji, Z., Ji, H., Zhu, H., Guan, Y. & Taverna, S. D., 2023, (Accepted/In press) In: Molecular Neurobiology.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sensory Receptor Cells 100%
  • Transcription Factors 70%
  • Chromatin 61%
  • RNA-Seq 54%
  • Spinal Ganglia 50%

• Immune activation and exhaustion marker expression on T-cell subsets in ART-treated adolescents and young adults with perinatal HIV-1 infection as correlates of viral persistence

  Huang, Y., Dhummakupt, A., Khetan, P., Nilles, T., Zhou, W., Mudvari, P., Szewczyk, J., Chen, Y. H., Boritz, E., Ji, H., Agwu, A. & Persaud, D., 2023, In: Frontiers in immunology. 14, 1007626.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • T-Lymphocyte Subsets 100%
  • HIV Infections 82%
  • HIV-1 81%
  • Young Adult 75%
  • DNA 23%

• Impact of Seasonal Coronavirus Antibodies on Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Responses in Solid Organ Transplant Recipients

  Karaba, A. H., Zhou, W., Li, S., Aytenfisu, T. Y., Johnston, T. S., Akinde, O., Eby, Y., Abedon, A. T., Alejo, J. L., Qin, C. X., Thompson, E. A., Garonzik, J., Blankson, J. N., Cox, A. L., Bailey, J. R., Klein, S. L., Pekosz, A., Segev, D., Tobian, A. A. R. & Werbel, W. A., Feb 1 2023, In: Clinical Infectious Diseases. 76, 3, p. E495-E498

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Severe Acute Respiratory Syndrome 100%
  • Coronavirus 97%
  • Transplant Recipients 72%
  • Vaccines 58%
  • Transplants 48%

• NF-κB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells

  Zhao, M., Chauhan, P., Sherman, C. A., Singh, A., Kaileh, M., Mazan-Mamczarz, K., Ji, H., Joy, J., Nandi, S., De, S., Zhang, Y., Fan, J., Becker, K. G., Loke, P., Zhou, W. & Sen, R., Sep 2023, In: Nature Immunology. 24, 9, p. 1552-1564 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • B-Cell Antigen Receptors 100%
  • NF-kappa B 83%
  • B-Lymphocytes 45%
  • Gene Expression 23%
  • RNA Sequence Analysis 22%

• The BAF chromatin complex component SMARCC1 does not mediate GLI transcriptional repression of Hedgehog target genes in limb buds

  Ramachandran, J., Chen, W., Lex, R. K., Windsor, K. E., Lee, H., Wang, T., Zhou, W., Ji, H. & Vokes, S. A., Dec 2023, In: Developmental biology. 504, p. 128-136 9 p.

  Research output: Contribution to journal › Article › peer-review

  • Limb Buds 100%
  • Hedgehogs 95%
  • Chromatin Assembly and Disassembly 85%
  • Chromatin 64%
  • Extremities 53%
• 2022

  Differential Cytokine Signatures of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Influenza Infection Highlight Key Differences in Pathobiology

  Karaba, A. H., Zhou, W., Hsieh, L. L., Figueroa, A., Massaccesi, G., Rothman, R. E., Fenstermacher, K. Z. J., Sauer, L., Shaw-Saliba, K., Blair, P. W., Robinson, M. L., Leung, S., Wesson, R., Alachkar, N., El-Diwany, R., Ji, H. & Cox, A. L., Jan 15 2022, In: Clinical Infectious Diseases. 74, 2, p. 254-262 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Severe Acute Respiratory Syndrome 100%
  • Coronavirus 97%
  • Human Influenza 71%
  • Cytokines 48%
  • Infections 37%

• Edaravone activates the GDNF/RET neurotrophic signaling pathway and protects mRNA-induced motor neurons from iPS cells

  Li, Q., Feng, Y., Xue, Y., Zhan, X., Fu, Y., Gui, G., Zhou, W., Richard, J-P., Taga, A., Li, P., Mao, X., Maragakis, N. J. & Ying, M., Dec 2022, In: Molecular neurodegeneration. 17, 1, 8.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Edaravone 100%
  • Glial Cell Line-Derived Neurotrophic Factor 87%
  • Amyotrophic Lateral Sclerosis 70%
  • Motor Neurons 64%
  • Messenger RNA 37%

• GLI transcriptional repression is inert prior to Hedgehog pathway activation

  Lex, R. K., Zhou, W., Ji, Z., Falkenstein, K. N., Schuler, K. E., Windsor, K. E., Kim, J. D., Ji, H. & Vokes, S. A., Dec 2022, In: Nature communications. 13, 1, 808.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Developmental 100%
  • Enhancer 97%
  • Acetylation 83%
  • activation 65%
  • gene expression 55%

• Hedgehog regulation of epithelial cell state and morphogenesis in the larynx

  Ramachandran, J., Zhou, W., Bardenhagen, A. E., Nasr, T., Yates, E. R., Zorn, A. M., Ji, H. & Vokes, S. A., Nov 2022, In: eLife. 11, e77055.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Hedgehogs 100%
  • Cell Death 81%
  • Larynx 80%
  • Hedgehog Proteins 76%
  • Morphogenesis 76%
• 2021

  A biomarker-authenticated model of schizophrenia implicating NPTX2 loss of function

  Xiao, M. F., Roh, S. E., Zhou, J., Chien, C. C., Lucey, B. P., Craig, M. T., Hayes, L. N., Coughlin, J. M., Markus Leweke, F., Jia, M., Xu, D., Zhou, W., Conover Talbot, J., Arnold, D. B., Staley, M., Jiang, C., Reti, I. M., Sawa, A., Pelkey, K. A., McBain, C. J., & 2 othersSavonenko, A. & Worley, P. F., Nov 2021, In: Science Advances. 7, 48, eabf6935.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Schizophrenia 100%
  • Biomarkers 79%
  • Synapses 75%
  • Parvalbumins 52%
  • Immediate-Early Genes 49%

• Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis

  Koldobskiy, M. A., Jenkinson, G., Abante, J., Rodriguez DiBlasi, V. A., Zhou, W., Pujadas, E., Idrizi, A., Tryggvadottir, R., Callahan, C., Bonifant, C. L., Rabin, K. R., Brown, P. A., Ji, H., Goutsias, J. & Feinberg, A. P., Apr 2021, In: Nature biomedical engineering. 5, 4, p. 360-376 17 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Methylation 100%
  • Pediatrics 83%
  • Information analysis 79%
  • DNA Methylation 68%
  • Gene expression 67%

• Distinct Cytokine and Chemokine Dysregulation in Hospitalized Children with Acute Coronavirus Disease 2019 and Multisystem Inflammatory Syndrome with Similar Levels of Nasopharyngeal Severe Acute Respiratory Syndrome Coronavirus 2 Shedding

  Peart Akindele, N., Kouo, T., Karaba, A. H., Gordon, O., Fenstermacher, K. Z. J., Beaudry, J., Rubens, J. H., Atik, C. C., Zhou, W., Ji, H., Tao, X., Vaidya, D., Mostafa, H., Caturegli, P., Blair, P. W., Sauer, L., Cox, A. L. & Persaud, D., Aug 15 2021, In: Journal of Infectious Diseases. 224, 4, p. 606-615 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Severe Acute Respiratory Syndrome 100%
  • Coronavirus 97%
  • Acute Disease 83%
  • Chemokines 72%
  • Cytokines 48%

• Egfr activates a taz-driven oncogenic program in glioblastoma

  Gao, M., Fu, Y., Zhou, W., Gui, G., Lal, B., Li, Y., Xia, S., Ji, H., Eberhart, C. G., Laterra, J. & Ying, M., Jul 1 2021, In: Cancer Research. 81, 13, p. 3580-3592 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • osimertinib 100%
  • Glioblastoma 92%
  • Epidermal Growth Factor 30%
  • epidermal growth factor receptor VIII 25%
  • Mitogens 15%

• Genome-wide prediction of chromatin accessibility based on gene expression

  Zhou, W. & Ji, H., Sep 1 2021, In: Wiley Interdisciplinary Reviews: Computational Statistics. 13, 5, e1544.

  Research output: Contribution to journal › Review article › peer-review

  • Chromatin 100%
  • Gene Expression 73%
  • Accessibility 73%
  • Genome 64%
  • Gene Regulation 61%

• Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

  Stephens, K. E., Zhou, W., Renfro, Z., Ji, Z., Ji, H., Guan, Y. & Taverna, S. D., Dec 2021, In: Journal of Neuroinflammation. 18, 1, 185.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Peripheral Nervous System 100%
  • Chromatin 81%
  • Spinal Ganglia 74%
  • Animal Models 66%
  • Chronic Pain 62%

• Metabolic programs define dysfunctional immune responses in severe COVID-19 patients

  Thompson, E. A., Cascino, K., Ordonez Suarez, A., Zhou, W., Vaghasia, A., Hamacher-Brady, A., Brady, N. R., Sun, I. H., Wang, R., Rosenberg, A. Z., Delannoy, M., Rothman, R., Fenstermacher, K., Sauer, L., Shaw Saliba, K., Bloch, E. M., Redd, A., Tobian, A. A. R., Horton, M., Smith, K., & 6 othersPekosz, A., D'Alessio, F. R., Yegnasubramanian, S., Ji, H., Cox, A. L. & Powell, J., Mar 16 2021, In: Cell Reports. 34, 11, 108863.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Coronavirus 100%
  • Metabolic 64%
  • Voltage-Dependent Anion Channel 1 45%
  • Lymphopenia 38%
  • T-Lymphocytes 24%

• Profiling Chromatin Accessibility at Single-cell Resolution

  Sinha, S., Satpathy, A. T., Zhou, W., Ji, H., Stratton, J. A., Jaffer, A., Bahlis, N., Morrissy, S. & Biernaskie, J. A., Apr 2021, In: Genomics, Proteomics and Bioinformatics. 19, 2, p. 172-190 19 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Chromatin 100%
  • Profiling 82%
  • Accessibility 73%
  • Plastic Property 67%
  • Heterogeneity 54%

• Reprogramming transcription factors Oct4 and Sox2 induce a BRD-dependent immunosuppressive transcriptome in GBM-propagating cells

  Ma, T., Hu, C., Lal, B., Zhou, W., Ma, Y., Ying, M., Prinos, P., Quiñones-Hinojosa, A., Lim, M., Laterra, J. & Li, Y., May 1 2021, In: Cancer Research. 81, 9, p. 2457-2469 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Transcriptome 100%
  • Immunosuppressive Agents 90%
  • Transcription Factors 81%
  • Immune Evasion 15%
  • Phenotype 14%
• 2020

  Altered 3D chromatin structure permits inversional recombination at the IgH locus

  Qiu, X., Ma, F., Zhao, M., Cao, Y., Shipp, L., Liu, A., Dutta, A., Singh, A., Braikia, F. Z., De, S., Wood, W. H., Becker, K. G., Zhou, W., Ji, H., Zhao, K., Atchison, M. L. & Sen, R., Aug 2020, In: Science Advances. 6, 33, eaaz8850.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Immunoglobulin Heavy Chains 100%
  • Genetic Recombination 73%
  • Chromatin 68%
  • Genes 30%
  • Immunoglobulin Heavy Chain Genes 30%
  2 Scopus citations

• GLI transcriptional repression regulates tissue-specific enhancer activity in response to hedgehog signaling

  Lex, R. K., Ji, Z., Falkenstein, K. N., Zhou, W., Henry, J. L., Ji, H. & Vokes, S. A., Jan 2020, In: eLife. 9, e50670.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Limb Buds 100%
  • Hedgehogs 95%
  • Enhancer 86%
  • Acetylation 76%
  • H3K27Ac 58%
  4 Scopus citations

• Single-cell ATAC-seq signal extraction and enhancement with SCATE

  Ji, Z., Zhou, W., Hou, W. & Ji, H., Jul 3 2020, In: Genome biology. 21, 1, 1713098.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Chromatin Immunoprecipitation Sequencing 100%
  • cell 47%
  • regulatory sequences 44%
  • cells 24%
  • Transposases 18%
  3 Scopus citations
• 2019

  Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq

  Zhou, W., Ji, Z., Fang, W. & Ji, H., Nov 4 2019, In: Nucleic acids research. 47, 19, p. E121

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA-Seq 100%
  • Chromatin Immunoprecipitation Sequencing 92%
  • Chromatin 75%
  • Cell Count 64%
  • Technology 28%
  7 Scopus citations

• Sex differences in gene regulation in the dorsal root ganglion after nerve injury

  Stephens, K. E., Zhou, W., Ji, Z., Chen, Z., He, S., Ji, H., Guan, Y. & Taverna, S. D., Feb 19 2019, In: BMC genomics. 20, 1, 147.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Spinal Ganglia 100%
  • Sex Characteristics 86%
  • Peripheral Nervous System 66%
  • Pain 53%
  • Wounds and Injuries 44%
  14 Scopus citations
• 2018

  Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus

  Qiu, X., Kumari, G., Gerasimova, T., Du, H., Labaran, L., Singh, A., De, S., Wood, W. H., Becker, K. G., Zhou, W., Ji, H. & Sen, R., Apr 5 2018, In: Molecular cell. 70, 1, p. 21-33.e6

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Immunoglobulin Heavy Chains 100%
  • Intergenic DNA 74%
  • Genetic Recombination 73%
  • Insulator Elements 61%
  • Gene Rearrangement 45%
  17 Scopus citations

• Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation

  Zhao, M., Joy, J., Zhou, W., De, S., Wood, W. H., Becker, K. G., Ji, H. & Sen, R., Sep 2018, In: PLoS biology. 16, 9, e2006347.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • NF-kappa B 100%
  • Kinetics 67%
  • kinetics 61%
  • gene expression 56%
  • Gene Expression 56%
  17 Scopus citations
• 2017

  Computational prediction of the global functional genomic landscape: Applications, methods, and challenges

  Zhou, W., Sherwood, B. & Ji, H., Jan 1 2017, In: Human Heredity. 81, 2, p. 88-105 18 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Explosive Agents 100%
  • Data Accuracy 82%
  • Genomics 79%
  • Quality Control 76%
  • Costs and Cost Analysis 48%
  1 Scopus citations

• Genome-wide prediction of DNase i hypersensitivity using gene expression

  Zhou, W., Sherwood, B., Ji, Z., Xue, Y., Du, F., Bai, J., Ying, M. & Ji, H., Dec 1 2017, In: Nature communications. 8, 1, 1038.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • gene expression 100%
  • genome 96%
  • Deoxyribonucleases 92%
  • Deoxyribonuclease I 88%
  • Transcriptome 67%
  12 Scopus citations

• Single-cell regulome data analysis by SCRAT

  Ji, Z., Zhou, W. & Ji, H., Sep 15 2017, In: Bioinformatics. 33, 18, p. 2930-2932 3 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Transcription factors 100%
  • Genes 66%
  • Deoxyribonucleases 66%
  • Heterogeneity 64%
  • Data analysis 62%
  19 Scopus citations
• 2015

  HOXB7 is an ERα cofactor in the activation of HER2 and multiple ER target genes leading to endocrine resistance

  Jin, K., Park, S., Teo, W. W., Korangath, P., Cho, S. S., Yoshida, T., Győrffy, B., Goswami, C. P., Nakshatri, H., Cruz, L. A., Zhou, W., Ji, H., Su, Y., Ekram, M., Wu, Z., Zhu, T., Polyak, K. & Sukumar, S., Sep 1 2015, In: Cancer discovery. 5, 9, p. 944-959 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • erbB-2 Genes 100%
  • Estrogen Receptors 89%
  • Breast Neoplasms 61%
  • Tamoxifen 51%
  • Genes 38%
  46 Scopus citations

• Mining of protein-protein interfacial residues from massive protein sequential and spatial data

  Wang, D. D., Zhou, W. & Yan, H., Jan 1 2015, In: Fuzzy Sets and Systems. 258, p. 101-116 16 p.

  Research output: Contribution to journal › Article › peer-review

  • Spatial Data 100%
  • Mining 92%
  • Extreme Learning Machine 79%
  • Protein 77%
  • Fuzzy Classifier 75%
  5 Scopus citations
• 2014

  Alpha shape and delaunay triangulation in studies of protein-related interactions

  Zhou, W. & Yan, H., Jan 2014, In: Briefings in bioinformatics. 15, 1, p. 54-64 11 p., bbs077.

  Research output: Contribution to journal › Article › peer-review

  • Triangulation 100%
  • Proteins 82%
  • Ligands 14%
  • DNA 11%
  • Atoms 11%
  16 Scopus citations
• 2013

  A survey on structural analysis of nucleosome core particles

  Yang, X., Zhou, W., Wang, D. D., Wu, Q. & Yan, H., 2013, In: Current Bioinformatics. 8, 1, p. 112-132 21 p.

  Research output: Contribution to journal › Article › peer-review

  • Structural Analysis 100%
  • Nucleosomes 93%
  • Histone 85%
  • Positioning 71%
  • Genomics 62%

• Identification of dna-binding and protein-binding proteins using enhanced graph wavelet features

  Zhu, Y., Zhou, W., Dai, D. Q. & Yan, H., Jul 2013, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10, 4, p. 1017-1031 15 p., 6606795.

  Research output: Contribution to journal › Article › peer-review

  • Protein Binding 100%
  • Carrier Proteins 97%
  • Protein 63%
  • Atoms 63%
  • Biomolecules 57%
  3 Scopus citations

• Personalized prediction of EGFR mutation-induced drug resistance in lung cancer

  Wang, D. D., Zhou, W., Yan, H., Wong, M. & Lee, V., 2013, In: Scientific reports. 3, 2855.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Drug Resistance 100%
  • Lung Neoplasms 86%
  • Mutation 61%
  • Investigational Therapies 44%
  • Machine Learning 41%
  28 Scopus citations

• Prediction of anti-EGFR drug resistance base on binding free energy and hydrogen bond analysis

  Zhou, W., Wang, D. D., Yan, H., Wong, M. & Lee, V., Oct 10 2013, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2013 - 2013 IEEE Symposium Series on Computational Intelligence, SSCI 2013. p. 193-197 5 p. 6595408. (Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2013 - 2013 IEEE Symposium Series on Computational Intelligence, SSCI 2013).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Hydrogen Bonds 100%
  • Binding Energy 95%
  • Drug Resistance 93%
  • Hydrogen bonds 83%
  • Free energy 72%
  6 Scopus citations

• Prediction of protein-protein interactions based on molecular interface features and the support vector machine

  Zhou, W., Yan, H., Fan, X. & Hao, Q., 2013, In: Current Bioinformatics. 8, 1, p. 3-8 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein-protein Interaction 100%
  • Support Vector Machine 79%
  • Protein 66%
  • Prediction 50%
  • Sequence Analysis 30%
  6 Scopus citations
• 2012

  Analysis of ligand binding sites using alpha shapes

  Zhou, W. & Yan, H., Dec 1 2012, Proceedings 2012 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2012. p. 536-540 5 p. 6377780. (Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Binding sites 100%
  • Ligands 94%
  • Proteins 65%
  • X ray crystallography 20%
  • Drug Development 16%

• Analysis of surface structures of hydrogen bonding in protein-ligand interactions using the alpha shape model

  Zhou, W., Yan, H. & Hao, Q., Aug 30 2012, In: Chemical Physics Letters. 545, p. 125-131 7 p.

  Research output: Contribution to journal › Article › peer-review

  • hydrogen bonds 100%
  • ligands 96%
  • Surface Structure 93%
  • proteins 76%
  • Shape 62%
  18 Scopus citations

• The relationship between geometric patterns of hydrogen bonds and periodic dinucleotides in nucleosome structures

  Guan, P. P., Zhou, W. & Yan, H., Nov 21 2012, In: Journal of Theoretical Biology. 313, p. 136-141 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Hydrogen Bonds 100%
  • Hydrogen bonds 83%
  • nucleosomes 74%
  • Hydrogen Bonding 73%
  • Nucleosomes 71%
  3 Scopus citations
• 2011

  Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences

  Wu, Q., Zhou, W., Wang, J. & Yan, H., Sep 7 2011, In: Journal of Theoretical Biology. 284, 1, p. 92-98 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Yeast 100%
  • DNA sequences 89%
  • DNA Sequence 87%
  • Dinucleotide 78%
  • Flexibility 68%
  4 Scopus citations

• Prediction of DNA-binding protein based on statistical and geometric features and support vector machines

  Zhou, W. & Yan, H., Oct 14 2011, In: Proteome Science. 9, SUPPL. 1, S1.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Support Vector Machine 100%
  • DNA-Binding Proteins 91%
  • Protein 33%
  • DNA 30%
  • Proteins 30%
  19 Scopus citations

• Prediction of protein-protein interactions using alpha shape modeling

  Zhou, W., Yan, H., Fan, X. & Hao, Q., 2011, 2011 International Symposium on Computational Models for Life Sciences, CMLS-11. p. 244-252 9 p. (AIP Conference Proceedings; vol. 1371).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • proteins 100%
  • predictions 67%
  • interactions 49%
  • correlation coefficients 13%
  • structural analysis 13%
  4 Scopus citations
• 2010

  A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling

  Zhou, W. & Yan, H., Aug 23 2010, In: Bioinformatics. 26, 20, p. 2541-2548 8 p., btq478.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Shape Modeling 100%
  • Protein 65%
  • DNA 64%
  • Molecular Recognition 62%
  • Surface Structure 60%
  19 Scopus citations

• Prediction of DNA-binding protein based on alpha shape modeling

  Zhou, W. & Yan, H., 2010, Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010. p. 23-28 6 p. 5706529. (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Carrier Proteins 100%
  • DNA-Binding Proteins 70%
  • DNA 64%
  • Proteins 22%
  • Membrane Proteins 17%
  2 Scopus citations

• Relationship between periodic dinucleotides and the nucleosome structure revealed by alpha shape modeling

  Zhou, W. & Yan, H., Apr 9 2010, In: Chemical Physics Letters. 489, 4-6, p. 225-228 4 p.

  Research output: Contribution to journal › Article › peer-review

  • chromatin 100%
  • nucleotides 96%
  • Dinucleotide 83%
  • positioning 76%
  • deoxyribonucleic acid 70%
  13 Scopus citations
• 2008

  A novel semantic-based CAD system for mammography

  Tang, X., Xu, X., Zhou, W. & Mao, Y., 2008, Proceedings of the International Conference on Computer Science and Information Technology, ICCSIT 2008. p. 97-101 5 p. 4624840. (Proceedings of the International Conference on Computer Science and Information Technology, ICCSIT 2008).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Mammography 100%
  • Computer aided design 64%
  • Semantics 52%
  • Computer aided diagnosis 19%
  • Standardization 14%

• Shape and boundary analysis for classification of breast masses

  Weiqiang, Z., Xiangmin, X. & Wei, H., 2008, Proceedings of the 2008 International Symposium on Computational Intelligence and Design, ISCID 2008. IEEE Computer Society, p. 42-46 5 p. 4725453. (Proceedings of the 2008 International Symposium on Computational Intelligence and Design, ISCID 2008; vol. 2).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Tumors 100%
  • Fractal dimension 58%