Publication List

May 1031, 10088

Google Citation Profile


2022


  1. Tian Y, Li J, Cheung TC, Tam V, Lau CG, Wang X, Chin YR. Akt3 promotes cancer stemness in triple-negative breast cancer through YB1-Snail/Slug signaling axis. Genes & Diseases. 2022;doi:10.1016/j.gendis.2022.08.006


  2. Esposito R, Polidori T, Meise DF, …, Zhu L, …, Wang X, Martinez I, Ochsenbein AF, Riether C, Johnson R. Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities. Cell Genomics. 2022; 100171.


  3. Lee IS, Zhu Z, Lee J, Park JO, Wu X, Ong T, Li SM, Wang X, Chao J and Goel A. A liquid biopsy signature predicts treatment response to fluoropyrimidine plus platinum therapy in patients with metastatic or unresectable gastric cancer: implications for precision oncology. Molecular Cancer. 2022;21: 9.


  4. Huang S†, Wu T†, Lau AY, Au C, Huang H, Wang X*, Jin YK*. Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis. iScience. 2021;24: 103247.


  5. Tan M†, Ma J†, Yang X†, You Q, Guo X, Li Y, Wang R, Han G, Chen Y, Qiu X*, Wang X*, Zhao L*. Quantitative proteomics reveals differential immunoglobulin-associated proteome (IgAP) in patients of acute myocardial infarction and chronic coronary syndromes. Journal of Proteomics. 2022;252: 104449.


  6. Wu J†, Liu Q†, Zhang X†, Tan M†, Li X, Liu P, Wu L, Jiao F, Lin Z, Wu X*, Wang X*, Zhao Y*, Ren J*. The interaction between STING and NCOA4 exacerbates lethal sepsis by orchestrating ferroptosis and inflammatory responses in macrophages. Cell Death Dis. 2022;13: 1–17.


  7. Mai S, Zhu X, Wan EYC, Wu S, Yonathan JN, Wang J, Li Y et al., Wang X, Chan K, Wu D, Xiong W. Postnatal eye size in mice is controlled by SREBP2-mediated transcriptional repression of Lrp2 and Bmp2. Development. 2022;149. doi:10.1242/dev.200633


  8. Hu J, Lai Y, Huang H, Ramakrishnan S, Pan Y, Ma VWS, et al., Chan K, Wang X, Chin Y. TCOF1 upregulation in triple-negative breast cancer promotes stemness and tumour growth and correlates with poor prognosis. Br J Cancer. 2022;126: 57–71


  9. Kota Nakamura†,Zhongxu Zhu†, Souvick Roy†,Eunsung Jun† et al., Wang X*, Song Cheol Kim*, Daniel Von Hoff*, Ajay Goel*. An exosome-based transscriptomic signature for noninvasive, early detection of patients with pancreatic ductal adenocarcinoma: A multicenter cohort study. Gastroenterology. 2022.


  10. Wu T†, Huang H†,Wang X. Dissecting super-enhancer heterogeneity: time to re-examine cancer subtypes? Trends Genet. 2022. doi:10.1016/j.tig.2022.06.006. .


  11. Adam, R. S., Poel, D., Moreno, L. F., Spronck, J. M. A., de Back, T. R., Torang, A., Barila, P. M. G., ten Hoorn, S., Markowetz, F., Wang X., Verheul, H. M. W., Buffart, T. E., & Vermeulen, L. Development of a miRNA-based classifier for detection of colorectal cancer molecular subtypes. Molecular Oncology. 2022.


  12. Kan, T., Zhang, S., Zhou, S., Zhang, Y., Zhao, Y., Gao, Y., Zhang, T., Gao, F., Wang X. Zhao, L., & Yang, M. Single-cell RNA-seq recognized the initiator of epithelial ovarian cancer recurrence. Oncogene 2022 ; Vol. 41, No. 6. pp. 895-906.


  13. Miyoshi J†, Zhu Z†, Luo A†, Toden S, Zhou X, Izumi D, Kanda M, Takayama T, Parker IM, Wang M, Gao F, Zaidi AH, Baba H, Kodera Y, Cui Y, Wang X*, Liu Z*, Goel A*. A microRNA-based liquid biopsy signature for the early detection of esophageal squamous cell carcinoma: a retrospective, prospective and multicenter study, Mol Cancer 2022;21: 1–13.


    14. 2021


  14. Yuma Wada, Mitsuo Shimada, Yuji Morine, Tetsuya Ikemoto, Yu Saito, Zhongxu Zhu, Xin Wang, Ane Etxart, Yangsoon Park, Luis Bujanda, In Ja Park, and Ajay Goel. Circulating miRNA Signature Predicts Response to Preoperative Chemoradiotherapy in Locally Advanced Rectal Cancer. JCO Precision Oncology. November 1 2021 (5):1788.


  15. Izumi D†, Zhu Z†, Chen Y†, Toden S, Huo X, Kanda M, Ishimoto T, Gu D, Tan M, Kodera Y, Baba H, Li W, Chen J*, Wang X*, Goel A*. A liquid biopsy assay for the early detection of gastric cancer: A retrospective and prospective, multicenter study, JAMA Network Open 2021, 4: e2121129–e2121129.


  16. Qi L, Wang W, Wu T, Zhu L, He L, Wang X*, Multi-Omics Data Fusion for Cancer Molecular Subtyping Using Sparse Canonical Correlation Analysis, Frontiers in Genetics 2021, doi:10.3389/fgene.2021.607817.


  17. Huang H†, Hu J†, Maryam A, Huang Q, Zhang Y, Ramakrishnan S, Li J, Ma VW, Cheuk W, So GYK, Wang W, Cho WCS, Zhang L, Chan M, Wang X*, Chin YR*, Defining super-enhancer landscape in triple-negative breast cancer by multi-omic profiling, Nature Communications 2021, 12:1–16.


  18. Kandimalla R†, Wang W†, Yu F, Zhou N, Gao F, Spillman M, Moukova L, Slaby O, Salhia B, Zhou S*, Wang X*, Goel A*. OCaMIR – A noninvasive, diagnostic signature for early stage ovarian cancer: a multi-cohort retrospective and prospective study. Clinical Cancer Research, 2021, doi:10.1158⁄1078-0432.CCR-21-0267.


  19. Chen Y†, Wu T†,Zhu Z†, Huang H, Zhang L, Goel A, Wang X*. An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine. Seminars in Cancer Biology , 2021, doi:10.1016/j.semcancer.2021.03.011.


  20. Shao X†, Tan M†, Xie Y, Wang T, Huang H, Zhang Y, Liu J, Zhang W, Wang X*, Deng X*. An integrated network of virulence-associated transcriptional regulators in Pseudomonas syringae. Cell Reports, 2021, 34:108920.


  21. Xie K†, Wang Z†, Qi L†, Zhao X, Wang Y, Qu J, Huang L, Zhang W, Yang Y*, Wang X*, Shi P*. Profiling MicroRNAs with Associated Spatial Dynamics in Acute Tissue Slices. ACS Nano, 2021, doi:10.1021/acsnano.0c09676


  22. Qi L, Ke J, Yu Z, Cao Y, Lai Y, Chen Y, Gao F*, Wang X*. Identification of prognostic spatial organization features in colorectal cancer microenvironment using deep learning on histopathology images. Medicine in Omics, 2021; 100008.


  23. Huang S, Choi MH, Huang H, Wang X, Chang YC, Kim JY. Demyelination regulates the circadian transcription factor BMAL1 to signal adult neural stem cells to initiate oligodendrogenesis. Cell Reports , 2020, 33: 108394.


  24. Zhang Y, Zhu L, Wang X*. NEM-Tar: a probabilistic graphical model for cancer regulatory network inference and prioritization of potential therapeutic targets from multi-omics data. Frontiers in Genetics, 2021;12: 540.


  25. Chen S†, Zhu Z†, Yang X, Liu L, He Y, Yang M, Guan X, Wang X*, Yun J*. Cleavage and Polyadenylation Specific Factor 1 Promotes Tumor Progression via Alternative Polyadenylation and Splicing in Hepatocellular Carcinoma. Frontiers in Cell and Developmental Biology, 2021;9: 340.


  26. Feng Z, Zhou F, Tan M, Wang T, Chen Y, Xu W, Li B, Wang X*, Deng X*, He M*. Targeting m6A Modification Inhibits Herpes Virus 1 Infection. Genes & Diseases 2021. doi:10.1016/j.gendis.2021.02.004


  27. Yang Z†, Wang W†, Zhao L†, Wang X, Gimple RC, Xu L, Wang Y*, Rich JN*, Zhou S*. Plasma Cells Shape the Mesenchymal Identity of Ovarian Cancers through Transfer of Exosome-Derived microRNAs. Science Advances 2021, 7(9):eabb0737.


  28. Du Y, Yan Y, Xie S, Huang H, Wang X, Ng R, Zhou MM, Qian C. Structural Mechanism of Bivalent Histone H3K4me3K9me3 Recognition by the Spindlin1/C11orf84 Complex in rRNA Transcription Activation. Nature Communications 2021, 12: 949.


    29. 2020


  29. Shao X, Xie Y, Zhang Y, Liu J, Ding Y, Wu M, Wang X, Deng X, Novel therapeutic strategies for treating Pseudomonas aeruginosa infection. Expert Opin Drug Discov. 2020;15: 1403–1423.


  30. Huang S, Choi MH, Huang H, Wang X, Chang YC, Kim JY, Demyelination regulates the circadian transcription factor BMAL1 to signal adult neural stem cells to initiate oligodendrogenesis, Cell Reports 2020, 33: 108394.


  31. Hua C, Wang T, Shao X, Xie Y, Huang H, Liu J, Zhang W, Zhang Y, Ding Y, Jiang L, Wang X, Deng X. Pseudomonas syringae dual-function protein Lon switches between virulence and metabolism by acting as both DNA-binding transcriptional regulator and protease in different environments. Environmental Microbiology 2020;22: 2968–2988.


  32. Zhu Z†, Han G†, Huang H†, He L, Chen Y, Ke J, Gao F, Vermeulen L, Wang X, book chapter, “Genome-wide discovery of microRNA biomarkers for cancer precision medicine”, In Detection Methods in Precision Medicine, Mengsu Yang and Michael Thompson, The Royal Society of Chemistry, 2020


  33. Wan Y†, Liu J†, Zhu L†, Kang TZ, Zhu X, Lis J, Ishibashi T, Danko C*, Wang X* & Chan K*. The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma. Sig Transduct Target Ther 5, 106 (2020).


  34. Wang Z†, Qi L†, Yang Y†, Lu M, Xie K, Zhao X, Cheung EHC, Wang Y, Jiang X, Zhang W*, Huang L*, Wang X* & Shi P*. High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity. Science Advances 2020, 6: eaba4971.


  35. Kan T, Wang W, Ip PP, Zhou S, Wong AS, Wang X & Mengsu Yang.Single-cell EMT-related transcriptional analysis revealed intra-cluster heterogeneity of tumor cell clusters in epithelial ovarian cancer ascites. Oncogene. 2020 doi:10.1038/s41388-020-1288-2


  36. Wan YCE†, Leung TCS†, Ding D†, Sun X, Liu J, Zhu L, Kang TZE, Yang D, Zhang YC, Zhang J, Qian C, Huen MSY, Li Q, Chow MZY, Zheng Z, Han J, Goel A, Wang X*, Ishibashi T*, Chan KM*. Cancer-associated histone mutation H2BG53D disrupts DNA–histone octamer interaction and promotes oncogenic phenotypes. Signal Transduction and Targeted Therapy 2020;5: 27


  37. Zhang Y†, Zhu L†, Wang X*. A Network-Based Approach for Identification of Subtype-Specific Master Regulators in Pancreatic Ductal Adenocarcinoma. Genes. 2020;11. doi:10.3390/genes11020155


  38. Dijk F*, Veenstra VL, Soer EC, Dings MPG, Zhao L, Halfwerk JB, Hooijer GK, Damhofer H, Marzano M, Steins A, Waasdorp C, Busch OR, Besselink MG, Tol JA, Welling L, van Rijssen LB, Klompmaker S, Wilmink HW, van Laarhoven HW, Medema JP, Vermeulen L, van Hooff SR, Koster J, Verheij J, van de Vijver MJ, Wang X*, Bijlsma MF*. Unsupervised class discovery in pancreatic ductal adenocarcinoma reveals cell-intrinsic mesenchymal features and high concordance between existing classification systems. Sci Rep 2020;10: 337


    39. 2019

  39. Ding X, He M, Chan AWH, Song QX, Sze SC, Chen H, Man MHK, Man K, Chan SL, Lai PBS, Wang X & Wong N. Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas.Gastroenterology2019, doi:10.1053/j.gastro.2019.09.005


  40. Gao F, Wang W, Tan M, Zhu L, Zhang Y, Fessler E, Vermeulen L & Wang X*. DeepCC: a novel deep learning-based framework for cancer molecular subtype classification.Oncogenesis 2019;8. 44.


  41. 354 authors, including, Gao F, Wang W & Wang X. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.Nature Communications 2019;10. 2674.
    42. https://doi.org/10.1038/s41467-019-09799-2


  42. Huang H†, Shao X†, Xie Y†, Wang T, Zhang Y, Wang X*, Deng X*, An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa, Nature Communications 2019,10: 2931


  43. Kandimalla R†, Gao F†, Li Y†, Huang H, Ke J, Deng X, Zhao L, Zhou S, Goel A* and Wang X*,RNAMethyPro: a biologically conserved signature of N6-methyladenosine regulators for predicting survival at pan-cancer level. npj Precision Oncology. 2019;3: 13.


  44. Kandimalla R†, Ozawa T†,Gao F†,Wang X*, Goel A* and the T1 Colorectal Cancer Study Group, Gene Expression Signature in Surgical Tissues and Endoscopic Biopsies Identifies High-risk T1 Colorectal Cancers,Gastroenterology 2019, DOI: https://doi.org/10.1053/j.gastro.2019.02.027


  45. Izumi D†,Gao F†, Toden S, Sonohara F, Kanda M, Ishimoto T, Kodera Y,Wang X*, Baba H and Goel A*, A genome-wide transcriptomic approach identifies a novel gene expression signature for the detection of lymph node metastasis in patients with early stage gastric cancer,EBioMedicine 2019, pii: S2352-3964(19)30063-5


  46. Chen H†,Gao F†, He M†, Ding XF, Wong AM, Sze SC, Yu AC, Sun T, Chan AWH,Wang X*, Wong N*, Long-read RNA Sequencing identifies Novel Splice Variants in Hepatocellular Carcinoma and Tumor‐specific Isoforms,Hepatology 2019; doi:10.1002/hep.30500


    47. 2018


  47. Lin X†, Duan X†, Jacobs C, Ullmann J, Chan CY, Chen S, Cheng SH, Zhao WN, Poduri A, Wang X*, Haggarty SJ*, Shi P*, High-throughput Brain Activity Mapping and Machine Learning as a Foundation for Systems Neuropharmacology, Nature Communications 2018;9:5142. (co-corresponding author) (more about the paper) News:


  48. Xu Z, Fang P, Xu B, Lu Y, Xiong J, Gao F, Wang X, Fan J, Shi P*, High-throughput Three-dimensional Chemotactic Assays Reveal Steepness-dependent Complexity in Neuronal Sensation to Molecular Gradients, Nature Communications 2018;9: 4745.


  49. Zhao L†, Wang W†, Xu L, Yi T, Zhao X, Wei Y, Vermeulen L, Goel A, Zhou S* and Wang X*, Integrative network biology analysis identifies miR-508-3p as the determinant for the mesenchymal identity and a strong prognostic biomarker of ovarian cancer, Oncogene 2018, doi:10.1038/s41388-018-0577-5 (co-corresponding author)(more about the paper)


  50. He L, Gomes AP†, Wang X†, Yoon SO, Lee G, Nagiec M, Cho S, Chavez A, Islam T, Yu Y, Asara JM, Kim BY, Blenis J. mTORC1 Promotes Metabolic Reprogramming by the Suppression of GSK3-Dependent Foxk1 Phosphorylation. Molecular Cell 2018, doi:10.1016/j.molcel.2018.04.024   (more about the paper)


  51. Kandimalla R†, Gao F†, Matsuyama T, Ishikawa T, Uetake H, Takahashi N, Yamada Y, Becerra C, Kopetz S, Wang X* and Goel A*. Genome-wide discovery and identification of a novel miRNA signature for recurrence prediction in stage II and III colorectal cancer. Clin Cancer Res 2018, doi:10.1158⁄1078-0432.CCR-17-3236   (more about the paper)


  52. Wang W†, Kandimalla R†, Huang H†, Zhu L, Li Y, Gao F, Goel A*, Wang X*, Molecular subtyping of colorectal cancer: recent progress, new challenges and emerging opportunities, Seminars in Cancer Biology 2018, doi:10.1016/j.semcancer.2018.05.002   (more about the paper)


  53. Zhao L, Huang S, Mei S, Yang Z, Xu L, Zhou N, Yang Q, Shen Q, Wang W, Le X, Lau WB, Lau B, Wang X, Yi T, Zhao X, Wei Y, Warner M, Gustafsson JA, Zhou S. Pharmacological activation of estrogen receptor beta augments innate immunity to suppress cancer metastasis. PNAS 2018, 115(16):E3673-E3681


  54. Zhao L†, Wang W†, Huang S†, Yang Z†, Xu L†, Yang Q†, Zhou X, Wang J, Shen Q, Wang C, Le X, Feng M, Zhou N, Lau WB, Lau B, Yao S, Yi T, Wang X, Zhao X, Wei Y and Zhou S. The RNA binding protein SORBS2 suppresses metastatic colonization of ovarian cancer by stabilizing tumor-suppressive immunomodulatory transcripts. Genome Biology 2018, 19(1):35   (more about the paper)


    55. 2017


  55. Sonohara F†, Gao F†, Iwata N, Kanda M, Koike M, Takahashi N, Yamada Y, Kodera Y, Wang X*, Goel A*, Genome-wide Discovery of a Novel Gene-expression Signature for the Identification of Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma, Annals of Surgery 2017, doi:10.1097/SLA.0000000000002622   (more about the paper)


  56. Xu Z, Wang W, Ren Y, Zhang W, Fang P, Huang L, Wang X and Shi P. Regeneration of cortical tissue from brain injury by implantation of defined molecular gradient of semaphorin 3A. Biomaterials 2018;157: 125-135, doi: 10.1016/j.biomaterials.2017.12.010   (more about the paper)


  57. Linnekamp JF†, van Hooff SR†, Prasetyanti PR, Kandimalla R, Buikhuisen JY, Fessler E, Ramesh P, Lee KAST, van Bochove GGW, de Jong JH, Cameron K, van Leersum R, Rodermond HM, Franitza M, Nürnberg P, Mangiapane LR, Wang X, Clevers H, Vermeulen L, Stassi G and Medema JP, Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models, Cell Death and Differentiation 2018, doi:10.1038/s41418-017-0011-5   (more about the paper)


  58. Ozawa T†, Kandimalla R†, Gao F†, Nozawa H, Hata K, Nagata H, Okada S, Izumi D, Baba H, Fleshman J, Wang X, Watanabe T, Goel A, A microRNA Signature Associated With Metastasis of T1 Colorectal Tumors to Lymph Nodes, Gastroenterology 2017, doi: 10.1053/j.gastro.2017.11.275   (more about the paper)


  59. Wang Y, Lin X, Chen X, Chen X, Xu Z, Zhang W, Liao Q, Duan X, Wang X, Liu M, Wang F, He J & Shi P, Tetherless near-infrared control of brain activity in behaving animals using fully implantable upconversion microdevices, Biomaterials 2017, 142, 136-148, doi: 10.1016/j.biomaterials.2017.07.017

    60. 2016


  60. Yu VWC, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT, Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells, Cell 2016, 167(5):1310-1322


  61. Trinh A, Trumpi K, De Sousa E Melo F, Wang X, de Jong JH, Fessler E, Kuppen PJK, Reimers MS, Swets M, Koopman M, Nagtegaal I, Jansen M, Hooijer GKJ, Offerhaus GJ, Kranenburg O, Punt CJ, Medema JP, Markowetz F, Vermeulen L, Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry, Clinical Cancer Research 2016, doi: 10.1158⁄1078-0432.CCR-16-0680


  62. Fessler E, Drost J, van Hooff SR, Linnekamp JF, Wang X, Jansen M, De Sousa E Melo F, Prasetyanti PR, IJspeert JEG, Franitza M, Nürnberg P, van Noesel CJM, Dekker E, Vermeulen L, Clevers H, and Medem JP, TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype, EMBO Molecular Medicine 2016, 8(7): 745–760, doi: 10.15252/emmm.201606184


  63. Fessler E, Jansen M, De Sousa E Melo F, Zhao L, Prasetyanti PR, Rodermond H, Kandimalla R, Linnekamp JF, Franitza M, van Hooff SR, de Jong JH, Oppeneer SC, van Noesel CJM, Dekker E, Stassi G, Wang X*, Medema JP*, and Vermeulen L*, A multidimensional network approach reveals microRNAs as determinants of the mesenchymal colorectal cancer subtype, Oncogene 2016, doi: 10.1038/onc.2016.134 (co-corresponding author)   (more about the paper)


  64. Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell APW, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T, Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin, Science 2016, 351(6270):285-289   (more about the paper)

    65. 2015


  65. Guinney J†, Dienstmann R†, Wang X†, de Reyniès A†, Schlicker A†, Soneson C†, Marisa L†, Roepman P†, Nyamundanda G†, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L & Sabine Tejpar, The consensus molecular subtypes of colorectal cancer, Nature Medicine 2015, 10.1038/nm.3967   (more about the paper)


  66. Alekseyenko AA†, Walsh EM†, Wang X†, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, and French CA, The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains, Genes Dev 2015, 29: 1507-1523   (more about the paper)


  67. Wang X and Markowetz F, “Joining the dots–network analysis of gene perturbation data”, book chapter, In Systems Genetics: linking phenotype and genotype, Markowetz F and Boutros M, Cambridge University Press, 2015


  68. Sadanandam A†, Wang X†, Felipe de Sousa E, Gray JW, Vermeulen L, Hanahan D, & Medema JP, Reconciliation of classification systems defining molecular subtypes of colorectal cancer, Cell Cycle 2014, 13(3): 353-357


  69. De Sousa E Mello, F†, Wang X†, Jansen M, Fessler E, Trinh A, et al., Poor prognosis colon cancer is defined by a distinct molecular subtype and develops from serrated precursor lesions, Nature Medicine 2013, 19(5): 614-618   (more about the paper)


  70. Wang X, Yuan K, Hellmayr C, Liu W and Markowetz F, Reconstructing evolving signaling networks by hidden Markov nested effects models, Annals of Applied Statistics 2014, 8(1): 448-480


  71. Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, et al., Diverse epigenetic strategies interact to control epidermal differentiation. Nature Cell Biology 2012, 14(7):753-763


  72. Wang X, Castro MA, Mulder KW and Markowetz F, Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PLoS Computational Biology 2012, 8(6):e1002566


  73. Castro MA, Wang X, Fletcher M, Ponder BAJ, Meyer KB, Markowetz F, RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations, Genome Biology 2012, 13:R29


  74. Wang X†, Terfve C†, Rose JC, Markowetz F, HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. Bioinformatics 2011, 27(6):879



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