Ming Hu Research Program

Research

Overview

I have developed data normalization method HiCNorm (PMID: 23023982) which has been widely used in the analysis of genome-wide chromatin interactomic data. I have also developed methods for inferring three-dimensional chromatin organization and its dynamics, detecting long-range chromatin interactions, and jointly analyzing compendium of chromatin interactomic data. I played a key role in the discovery of topologically associating domains (TADs) (PMID: 22495300) and frequently interacting regions (FIREs) (PMID: 27851967). My work on a compendium of chromatin contact maps across 21 human cell lines and primary tissues (PMID: 27851967) has been selected as a “Research Highlight” by Nature Reviews Genetics (PMID: 27956750). I have published a review paper on chromosome architecture in Nature Reviews Molecular Cell Biology (PMID: 27580841). I have developed MAPS, a model-based method to identify long-range chromatin interactions from PLAC-Seq and HiChIP experiments (PMID: 30986246), which as been approved as the production pipeline for PLAC-seq and HiChIP data in the 4D Nucleome project. I have performed the first study of chromatin interactome variations across multiple individuals (PMID: 31779666). 

Most recently, I performed integrative analysis of multi-omics data from developing human cortex and discovered super-interactive promoters, which fine-tune transcription in a cell-type-specific manner. This work is published in Nature (PMID: 33057195). I have developed SnapHiC, the first method to identify chromatin loops from single cell Hi-C data, which is published in Nature Methods (PMID: 34446921). I have also developed methods for analyzing ChIP-seq data, bulk cell RNA-seq data and single cell RNA-seq data. As a biostatistician, I have contributed to multiple clinical studies in the area of ophthalmology and emergency medicine.

Collaboration

Dr. Justis Ehlers at Cole Eye Institute, Cleveland Clinic Foundation

Dr. Bing Ren's lab at University of California San Diego and Ludwig Institute of Cancer Research

Dr. Cornelis Murre's lab at University of California San Diego

Dr. Yun Li's lab at University of North Carolina Chapel Hill

Dr. Wei Chen's lab at Children's Hospital of Pittsburgh and University of Pittsburgh Medical Center

Dr. Yin Shen's lab at University of California San Francisco 

Software

• MAPS
  • Model-based analysis of long-range chromatin interactions from PLAC-Seq and HiChIP experiments
• BAMM-SC
  • a Bayesian mixture model for clustering droplet-based single cell transcriptomic data from multiple studies
• DIMM-SC
  • a Dirichlet mixture model for clustering droplet-based single cell transcrip tomic data
• Hugin
  • (Hi-C Unifying Genomic INterrogator): a genome browser of the integrative analysis of Hi-C data, SNP data and epigenetic data from 7 human cell lines and 14 human tissues
• FastHiC
  • a fast algorithm to detect long-range chromosomal interactions from Hi-C data
• hichelix
  • inferring spatial organizations of chromosomes via helix models
• HiView
  • a genome browser for the integrative analysis of Hi-C data, SNP data and epigenetic data
• HMRFBayesHiC
  • A hidden Markov random field based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data
• Bayesian 3D constructor for Hi-C data (BACH)
  • infer chromosome 3D structures and characterize chromatin structural variations
• HiCNorm
  • removing biases in Hi-C data via Poisson regression
• GPUmotif
  • An ultra-fast and energy-efficient motif analysis program using graphics processing units
• Poisson Mixed-Effects Regression for RNA-Seq Data (POME):
  • quantifying exon-level gene expression in RNA-Seq
• Hybrid Motif Sampler (HMS)
  • de novo motif discovery using ChIP-Seq data
• Bayesian Expression Search Tool (BEST)
  • query large scale microarray compendium datasets
• FIREcaller
  • An R package for detecting frequently interacting regions from Hi-C data
• TWO-SIGMA
  • TWO-component SInGle cell Model-based Association method

Selected Publications

First author and co-corresponding author papers (bold lists Hu lab memebers)

37. Quaid K, Xing X, Chen Y, Miao Y, Nielson A, Selvamani V, Tran A, Cui X#, Hu M# and Wang T# (2024). iPSCs and iPS-derived cells as a model of the relationship between genetic and epigenetic variation in humans. Accepted in principle. Nature Communications. #Co-corresponding author.

36. Murre C#, Patta I, Mishra S and Hu M# (2024). Constructing polymorphonuclear cells: chromatin folding shapes nuclear morphology. In press. Trends in Immunology. #Co-corresponding author.

35. Liu W*, Zhong W*, Giusti-Rodriguez P, Wang G, Hu M# and Li Y# (2024). SnapHiC-G: identifying long-range enhancer-promoter interactions from single cell Hi-C data via a global background model. Breifings in Bioinformatics. 2595):bbae426. Co-first author. #Co-corresponding author.

34. Yu H, Wu D, Mishra S, Shen G, Sun H, Hu M# and Li Y# (2024). SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. Communications Biology. 7(1):834. #Co-corresponding author.

33. Yu M*,#, Zemek N*, Chen Z*, Juric I, Hu R, Raviram R, Abnousi A, Fang R, Zhang Y, Gorkin DU, Li Y, Zhao Y, Lee L, Mishra S, Schmitt AD, Qiu Y, Dickel DE, Visel A, Pennacchio LA, Hu M# and Ren B# (2024). Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. In press. Nature Structural & Molecular Biology. *Co-first author. #Co-corresponding author.

32. Patta I, Zand M, Lee L, Mishra S, Bortnick A, Lu H, Prusty A, McArdle S, Mikulski Z, Wang H, Cheng C, Fisch K# , Hu M# and Murre C# (2024). Nuclear morphology is shaped by loop extrusion programs. Nature. 627(8002):196-203. #Co-corresponding author.

31. Lee L*, Yu M*, Li X, Zhu C, Zhang Y, Yu H, Chen Z, Mishra S, Ren B, Li Y# and Hu M# (2023). SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C data. Briefings in Bioinformatics. 24(5):bbad315. *Co-first author. #Co-corresponding author.

30. Lee L, Yu H, Jia B, Jussila A, Zhu C, Chen J, Xie L, Hafner A, Mishra S, Wang D, Strambio-De-Castillia C, Boettiger A, Ren B, Li Y# and Hu M# (2023). SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Nature Communications. 14(1):4873. #Co-corresponding author. The abstract of this work has been selected as a Reviewers' Choice Abstract in the ASHG 2022 annual meeting because reviewers scored it in the top 10% of poster abstracts.

29. Rosen J*, Lee L*, Abnousi A, Chen J, Wen J, Hu M# and Li Y# (2023). HPTAD: a computational method to identify topologically associating domains from HiChIP and PLAC-seq data. Computational and Structural Biotechnology Journal. Volumn 21, Pages 931-999. *Co-first author. #Co-corresponding author.

28. Barajas-Mora EM, Lee L, Lu H, Valderrama JA, Bjanes E, Zizet V, Feeney AJ, Hu M# and Murre C# (2022). Enhancer-instructed nuclear repositioning of Vk genes orchestrates rearrangement in a recombination hub to combat bacterial infection. Nature Immunology. 24, 320-336. #Co-corresponding author.

27. Zhong W*, Liu W*, Chen J, Sun Q, Hu M# and Li Y# (2022). Understanding the function of regulatory DNA interactions in interpretation of non-coding GWAS variants. Frontiers in Cell and Developmental Biology. 10:957292. *Co-first author. #Co-corresponding author.

26. Li X*, Lee L*, Abnousi A, Yu M, Liu W, Huang L, Li Y# and Hu M# (2022). SnapHiC2: a computationally efficient loop caller for single cell Hi-C data.  Computational and Structural Biotechnology Journal. 20:2778-2783. *Co-first author. #Co-corresponding author.

25. Huang L*, Yang Y*, Li G, Jiang M, Wen J, Abnousi A, Rosen J, Hu M# and Li Y# (2022). A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. Briefings in Bioinformatics. 23(3):bbac145. *Co-first author. #Co-corresponding author.

24. Liu W*, Zhong W*, Chen J, Huang B, Hu M# and Li Y# (2022). Understanding regulatory mechanisms of brain function and disease through 3D genome organization. Genes. 13(4), 586. *Co-first author. #Co-corresponding author.

23. Yu M, Li Y and Hu M* (2022). Mapping chromatin loops in single cells. Trends in Genetics. 38(7):637-640. *Corresponding author.

22. Yu M*, Abnousi A*, Zhang Y, Li G, Lee L, Chen Z, Fang R, Lagler T, Yang Y, Wen J, Sun Q, Li Y, Ren B# and Hu M# (2021). SnapHiC: a computational pipeline to identify chromatin loops from single cell Hi-C data. Nature Methods. 18(9):1056-1059. *Co-first author. #Co-corresponding author.

21. Liu W*, Yang Y*, Abnousi A, Zhang Q, Kubo N, Martin J,Li Y# and Hu M# (2021). MUNIn: a statistical framework for identifying long-range chromatin interactions from multiple samples. Human Genetics and Genomics Advances. 2(3):100036. *Co-first author. #Co-corresponding author.

20. Song M*, Pebworth M*, Yang X*, Abnousi A, Fang C, Wen J, Rosen J, Choudhary M, Cui X, Jones I, Bergenholtz S, Ugomma CE, Juric I, Li B, Maliskova L, Lee J, Liu W, Pollen A, Li Y, Wang T, Hu M*,#, Kriegstein A# and Shen Y# (2020). Cell-type-specific 3D epigenomes in the developing human cortex. Nature. 587(7835):644-649. *Co-first author. #Co-corresponding author.

19. Crowley C, Yang Y*, Qiu Y, Hu B, Abnousi A, Lipinski J, Plewczynski D, Won H, Di W, Ren B, Hu M* and LI Y* (2020). FIREcaller: detecting frequently interacting regions from Hi-C data. Computational and Structural Biotechnology Journal. 19:355-362. *Co-corresponding author.

18. Gorkin DU*, Qiu Y*, Hu M*,#, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Sebat J, Li Y, Hansen KD and Ren B#. (2019) Common DNA sequence variation influences 3-dimensional architecture of the human genome. Genome Biology. 20(1):255. *Co-first author. #Co-corresponding author.

17. Yu J, Hu M* and Li C*. (2019) Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes. BMC Genetics. 20(1):43. *Co-corresponding author.

16. Juric I*, Yu M*, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Yang Y, Li Y, Ren B# and Hu M# (2019). MAPS: model-based analysis of long-range chromatin interactions from PLAC-Seq and HiChIP experiments. PLOS Computational Biology. 15(4):e1006982. *Co-first author. #Co-corresponding author.

15. Sun Z, Chen L, Xin H, Jiang Y, Huang Q, Cillo AR, Tabib T, Kolls JK, Bruno TC, Lafyatis R, Vignali DAA, Chen K, Ding Y*, Hu M* and Chen W*. (2019) BAMM-SC: a Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies. Nature Communications. 10(1):1649. *Co-corresponding author. This paper has been selected as one of the International Biometric Society Eastern North American Regions (ENAR) Distinguished Student Paper Awards for the 2019 ENAR Spring Meeting in Philadelphia, PA.

14. Zhang R, Hu M*, Zhu Y*, Qin ZS, Deng K and Liu JS. (2018) Inferring spatial organization of individual topologically associated domains via piecewise helical model. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 17(2), 647-656. *Co-corresponding author.

13. Sun Z, Wang T, Deng K, Wang X, Layfatis R, Ding Y, Hu M* and Chen W* (2017). DIMM-SC: A Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. Bioinformatics. 34(1): 139-146. *Co-corresponding author.

12. Martin J, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, Hu M* and Li Y* (2017) HUGIn: Hi-C unifying genomic interrogator. *Bioinformatics. 33(23): 3793-3795. Co-corresponding author.

11. Schmitt AD, Hu M* and Ren B* (2016) Genome-wide mapping and analysis of chromosome architecture. Nature Reviews Molecular Cell Biology. 17: 743-755. *Co-corresponding author.

10. Schmitt AD*, Hu M*, #, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL and Ren B#. (2016) A compendium of chromatin contact maps reveal spatially active regions in the human genome. Cell Reports. 17(8): 2042-2059. *Co-first author. #Co-corresponding author. Full paper.

9. Xu Z, Zhang G, Wu C, Li Y* and Hu M*. (2016) FastHiC: a fast algorithm to detect long-range chromosomal interactions from Hi-C data. Bioinformatics. 32(17): 2692-2695. *Co-corresponding author. FastHiC software .

8. Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Feng Y, Li Y* and Hu M*. (2016) HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. BMC Research Notes. 9(1): 159. *Co-corresponding author. HiView software

7. Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin ZS, Hu M* and Li Y*. (2016) A hidden Markov random field based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Bioinformatics. 32(5): 650-656. *Co-corresponding author.

6. Hu M, Deng K, Qin ZS and Liu JS. (2013) Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data. Quantitative Biology, 1(2): 156-174. Abstract. Full paper. Featured cover image for this issue in Quantitative Biology. Selected as one of the two featured articles for this issue in Quantitative Biology.

5. Hu M, Deng K, Qin ZS, Dixon J, Selvaraj S, Fang J, Ren B and Liu JS. (2013) Bayesian inference of spatial organizations of chromosomes. PLoS Computational Biology, 9(1): e1002893. Abstract. Full paper. Download software BACH and BACH-MIX.

4. Hu M, Deng K, Selvaraj S, Qin ZS, Ren B and Liu JS. (2012) HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics, 28(23): 3131-3133. Abstract. Full paper. Download software HiCNorm.

3. Hu M, Zhu Y, Taylor JMG, Liu JS and Qin ZS. (2012) Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. Bioinformatics, 28(1): 63-68. Abstract. Full paper. Download software POME.

2. Hu M, Yu J, Taylor JMG, Chinnaiyan AM and Qin ZS. (2010) On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Research, 38(7), 2154-2167. Abstract. Full paper. Download software HMS.

1. Hu M and Qin ZS. (2009) Query large scale microarray compendium datasets using a model-based bayesian approach with variable selection. PLoS One, 4(2): e4495. Abstract. Full paper. Download software BEST.

Collaboration papers

80. Cui X, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Yang H, Fair T, Ye Z, Abnousi A, Mishra S, Hu M, Pollen AA, Pollard KS and Shen Y (2024) Comparative characterization of human accelerated regions in excitatory neurons. Accepted in principle. Nature.

79. Catta-Preta R, Lindtner S, Ypsilanti A, Seban N, Price JD, Abnousi A, Su-Feher L, Wang Y, Cichewicz K, Boerma SA, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio L, Dickel DE, Rubenstein JLR and Nord AS (2024). Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis. In press. Developmental Cell.

78. Chang L, Xie Y, Taylor B, Wang Z, Sun J, Armand E, Mishra S, Xu J, Tastemel M, Lie A, Gibbs Z, Tan TR, Bejar R, Chen CC, Furnari FB, Hu M and Ren B (2024). Droplet Hi-C for fast and scalable profiling of chromatin architecture in single cells. In press. Nature Biotechnology. 

77. Yordi S, Cakir Y, Kalra G, Cetin H, Hu M, Abraham J, Reese J, Srivastava SK and Ehlers JP (2024). Ellipsoid zone integrity and visual funciton in dry age-related macular degeneration. Journal of Personalized Medicine. 14(5):543.

76. Liu X, Xin D, Zhong X, Zhao C, Li Z, Zhang L, Dourson AJ, Lee L, Mishra S, Bayat AE, Nicholson E, Seibel WL, Yan B, Mason J, Turner B, Gonsalvez DG, Ong W, Chew SY, Ghosh B, Yoon SO, Xin M, He Z, Tchieu J, Wegner M, Nave KA, Franklin RJM, Dutta R, Trapp BD, Hu M, Smith MA, Jankowski MP, Barton SK, He X and Lu QR (2024). Small-molecular-induced rejuvenation promotes SREBP condensation and overcomes barries to CNS myelin regernation. Cell. 187(10):2465-2484.e22.

75. Fletez-Brant K, Qiu Y, Gorkin DU, Hu M and Hansen KD. Removing unwanted variation between samples in Hi-C experiments (2024). Removing unwanted variantion between samples in Hi-C experiments. Briefings in Bioinformatics. 25(3):bbae217.

74. Guo F, Zhang L, Yu Y, Gong L, Tao S, Werder RB, Mishra S, Zhou Y, Anamika WJ, Lao T, Inuzuka H, Zhang Y, Pham B, Liu T, Tufenkjian T, Richmod B, Wei W, Mou H, Wilson AA, Hu M, Chen W and Zhou X (2024). Identification of a distal enhancer regulating Hedgehog interacting protein gene in human lung epithelial cells. eBioMedicine. Volume 101, 105026.

73. Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Liu W, Lee L, Tang X, He W, Islam N, Jain A, Chiu Y, Cao S, Meyer-Gauen S, Hook M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz and Chen Y (2023). CRISPR-Case9-based functional interrogation of unconvertional translatome reveals human cancer dependency on cryptic non-cannoical open reading frames. Nature Structural & Molecular Biology. 30(12):1878-1892.

72. Hu X, Wu X, Berry K, Zhao C, Xin D, Ogurek S, Liu X, Zhang L, Luo Z, Sakabe M, Trubicka J, Lastowsk M, Szulzewsky F, Holland E, Lee L, Hu M, Xin M and Lu Q (2022). Nuclear condensates of YAP fusion proteins alter transcription to drive ependymoma tumorigenesis. Nature Cell Biology. 25(2):323-336.

71. Xu J, Mao C, Hou Y, Luo Y, Binder JL, Zhou Y, Bekris L, Shin J, Hu M, Wang F, Eng C, Oprea TI, Flanagan ME, Pieper AA, Cummings J, Leverenz JB and Cheng F (2022). Readily interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer's disease. Cell Reports. 41(9), 111717.

70. Kalra G, Talcott KE, Kaiser S, Uguegbu O, Hu M, Srivastava SK and Ehlers JP (2022). Automated machine learning detection of hydroxychloroquine toxicity and prediction of future toxicity using higher order OCT biomarkers. Ophthalmology Retina. 6(12): 1241-1252.

69. Arepalli S, Wykoff CC, Abraham JR, Lunasco L, Yu H, Hu M, Srivastava SK, Reese JL, Brown DM and Ehlers JP (2022). Longitudinal analysis of aqueous humor cytokine expression and OCT-based imaging biomarkers in retinal vein occlusions treated with anti-vascular endothelial growth factor therapy in the IMAGE DME study. Eye. 37(9):1928-1935.

68. Jiang AC, Sevgi DD, Mugnaini C, Whitney J, Srivastava SK, Talcott KE, Hu M, Reese JL and Ehlers JP (2022). Predictive assessment of quantitative ultra-widefield angiographic features for future need for anti-VEGF therapy in diabetic eye disease. Journal of Personalized Medicine. 12(4):608.

67. Ehlers J, Patel N, Kaiser P, Heier J, Brown D, Meng X, Reese J, Lunasco L, Le T, Hu M and Srivastava SK (2022). The association of fluid volatility with subretinal hyperreflective material and ellipsoid zone integrity in neovascular AMD. Investigative Ophthalmology & Visual Science. Vol 63, 17.

66. Rowland B, Huh R, Hou Z, Crowley C, Wen J, Shen Y, Hu M, Giusti-Rodriguez P, Sullivan PF and Li Y (2022). THUNDER: a reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. PLOS Genetics. 18(3):e1010102.

65. Buren EV, Hu M, Cheng L, Wrobel J, Wihelmsen K, Su L, Li Y and Wu D (2022). TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation. Briefings in Bioinformatics. 23(3):bbac084.

64. Wen J, Lagler T, Sun Q, Yang Y, Chen J, Harigaya Y, Sankaran V, Hu M, Reiner A, Raffiel L and Li Y (2021). Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types. PLOS Genetics. 18(1):e1009984. 

63. Ypsilanti A, Pattabiraman K, Catto-Pretta R, Golonzhka O, Lindtner S, Tang K, Jones I, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson C, Zeng H, Barozzi I, Nord A and Rubenstein J (2021). Transcriptional network orchestrating regional patterning of cortical progenitors. Proceedings of the National Academy of Sciences of the United States of America. 118(51):e2024795118.

62. Babiuch A, Wykoff C, Yordi S, Yu H, Srivastava SK, Hu M, Le TK, Lunasco L, Resse J, Nittala M, Sadda S and Ehlers JP (2021). The two-year leakage index and quantitative microaneurysm results of the RECOVERY study: quantitative ultra-widefield findings in proliferative diabetic retinopathy treated with intravitreal aflibercept. Journal of Personalized Medicine. 11(11), 1126.

61. Rosen J, Yang Y, Abnousi A, Chen J, Song M, Jones I, Shen Y, Hu M and Li Y (2021). HPrep: quantifying reproducibility in HiChIP and PLAC-seq datasets. Current Issues in Molecular Biology. 43(2), 1156-1170.

60. Sevgi D, Srivastava SK, Whitney J, O'Connell M, Kar S, Hu M, Reese J, Madabhushi A and Ehlers J (2021). Characterization of ultra-widefield angiographic vascular features in diabetic retinopathy with automated severity classification. Ophthalmology Science. 1(3):100049.

59. Wang F, Wang Y, Zhang K, Hu M and Zhang H (2021). Spatial heterogeneity modeling of water quality based on random forest regression and model interpretation. Environmental Research. 202:111660.

58. Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones I, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, Li G, Li Y, Hu M, Ren B, Wang W and Shen Y (2021). Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science Advances. 7(38)eabi4360.

57. Abraham J, Wykoff C, Apepalli S, Lunasco L, Yu H, Martin A, Mugnaini C, Hu M, Reese J, Srivastava S, Brown D and Ehlers J (2021). Exploring the angiographic-biologic phenotype in the IMAGINE DME study: quantitative UWFA and cytokine expression. British Journal of Ophthalmology. 160(10):1444-1449. 

56. Mokarram M, Pourghasemi HR, Hu M and Zhang H (2021). Determining and forecasting drought-prone areas in southwestern Iran using fuzzy-AHP method coupled with CA-Markov model. Science of the Total Environment. 781:146703.

55. Huang H, Zhu Q, Jussila A, Han Y, Bintu B, Kern C, Conte M, Zhang Y, Bianco S, Chiariello A, Yu M, Hu R, Tastemel M, Juric I, Hu M, Nicodemi M, Zhuang X and Ren B (2021). CTCF mediates dosage and sequence-context-dependent transcriptional insulation through formation of local chromatin domains. Nature Genetics. 53, 1064-1074.

54. Ehlers JP, Zahid R, Kaiser PK, Heier JS, Brown DM, Meng X, Reese JL, Le T, Lunasco L, Hu M and Srivastava SK (2021). Longitudinal assessment of ellipsoid zone integrity, subretinal hyperreflective material, and sub-RPE disease in neovascular AMD. Ophthalmology Retina. S2468-6530(21)00066-X.

53. Ehlers JP, Clark J, Uchida A, Figueiredo N, Babiuch A, Talcott KE, Lunasco L, Le TK, Meng X, Hu M, Resse JL, and Srivastava SK (2021). Longitudinal higher-order OCT assessment of quantitative fluid dynamics and the total retinal fluid index in neovascular AMD. Translational Vision Science & Technology. 10(3):29.

52. Lagler T, Abnousi A, Hu M, Yang Y and Li Y (2021). HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test. American Journal of Human Genetics. Volume 108, Issue 2, pages 257-268.

51. Ehlers JP, Uchida A, Sevgi D, Hu M, Reed K, Berliner A, Vitti R, Chu K and Srivastava SK (2020) Retinal fluid volatility associated with interval tolerance and visual outcomes in diabetic macular edema in the VISTA phase III trial. American Journal of Ophthalmology. Volume 224, page 217-227.

50. Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker J, Conte M, Gorkin D, Yu M, Li B, Dixon J, Hu M, Nicodemi M, Zhao H and Ren B (2020). Promoter-proximal CTCF-binding promotes long-range-enhancer dependent gene activation. Nature Structural & Molecular Biology. 28(2):152-161.

49. Buren EV, Hu M, Weng C, Jin F, Li Y, Wu D and Li Y (2020). TWO-SIGMA: a novel TWO-component SInGle cell Model-based Association method for single-cell RNA-seq data. Genetic Epidemiology. Volume 45, Issue 2, 142-153.

48. Abraham J, Wykoff C, Arepalli S, Lunasco L, Yu H, Hu M, Reese JL, Srivastava SK, Brown D and Ehlers JP (2020). Aqueous cytokine expression and higher-order OCT biomarkers: assessment of the anatomic-biologic bridge in the IMAGINE DME study. American Journal of Ophthalmology. 222:328-339.

47. Babiuch A, Wykoff CC, Hach J, Srivastava S, Talcott K, Yu H, Nittala M, Sadda S, Ip MS, Le T, Hu M, Reese JL and Ehlers JP (2020). Longitudinal panretinal microaneurysm dynamics on ultra-widefield fluorescein angiography in eyes treated with intravitreal aibercept for proliferative diabetic retinopathy in the RECOVERY study. British Journal of Ophthalmology. 105(8):1111-1115.

46. Liu C, Abnousi A, Bazeley P, Ni Y, Morley M, Morvec C, Hu M and Tang W (2020). Global analysis of histone modi cations and long-range chromatin interaction revealed the differential cistrome changes and novel transcriptional players in human dilated cardiomyopathy. Journal of Molecular and Cellular Cardiology. 145:30-42.

45. Lu L, Liu X, Huang WK, Giusti-Rodriguez P, Cui J, Zhang S, Xu W, Wen Z, Ma S, Rosen J, Xu Z, Bartels C, Kawaguchi R, Hu M, Scacheri P, Rong Z, Li Y, Sullivan P, Song H, Ming G, Li Y and Jin F. (2020) Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases. Molecular Cell. 79(3):521-534.

44. Babiuch AS, Uchida A, Hu M, Mehnaz K, Srivastava SK, Singh RP, Kaiser PK, Rachitskaya A, Reese JL and Ehlers JP (2020). Use of OCTA capillary perfusion density measurements to detect and grade macular ischemia. Ophthalmic Surgery, Lasers and Imaging Retina. 51(4):S30-S36.

43. Figueiredo N, Talcott KE, Srivastava SK, Hu M, Rachitskay A, Sharma S, Singh RP, Yuan A, Reese JL and Ehlers JP (2020). Conventional microscope-integrated intraoperative OCT versus digitally enabled intraoperative OCT in vitreorential surgery in the DISCOVER study. Ophthalmic Surgery, Lasers and Imaging Retina. 51(4):S37-S43.

42. Browne AW, Ansari W, Hu M, Baynes K, Lowder CY, Ehlers JP and Srivastava SK (2020). Quantitative analysis of ellipsoid zone in acute posterior multifocal placoid pigment epitheliopathy. Journal of VitreoRential Diseases. 4(3): 192-201.

41. Babiuch AS, Wyko CC, Srivastava SK, Talcott KE, Zhou B, Hach J, Hu M, Reese JL and Ehlers JP (2020). Retinal leakage index dynamics on ultra-wide field fluorescein angiography in eyes treated intravitreal aibercept for proliferative diabetic retinopathy in the RECOVERY study. Retina. 40(11):2175-2183.

40. Zhu C, Yu M, Huang H, Juric I, Abnousi A, Lucero J, Behres M, Hu M and Ren B. (2019) An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nature Structural & Molecular Biology. 26(11):1063-1070.

39. Venkat AG, Singh RP, Eisengart J, Hu M and Babiuch A (2019). Trends in neovascular glaucoma management: practice patterns of glaucoma and retina specialists in the United States. American Journal of Ophthalmic Clinical Trials. 2019.2;7.

38. Figueiredo N, Srivastava S, Singh RP, Babiuch A, Sharma S, Rachitskaya A, Talcott K, Reese J, Hu M and Ehlers JP (2019). Longitudinal panretinal leakage and ischemic indices in retinal vascular disease following aflibercept therapy: The PERMEATE study. Ophthalmology Retina. 4(2), 154-163.

37. Wu S, Turner K, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law J, Verhaak R, Hu M, Furnari F, Chang H, Ren B, Bafna V and Mischel P (2019). Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 575(7784):699-703.

36. Jiang A, Srivastava S, Hu M, Figueiredo N, Babiuch A, Boss J, Reese J and Ehlers JP (2019). Quantitative ultra-widefield angiographic features and associations with diabetic macular edema. Ophthalmology Retina. 4(1), 49-56.

35. Ehlers JP, Uchida A, Hu M, Figueiredo N, Kaiser P, Heier JS, Brown DM, Boyer DS, Do DV, Gibson A, Saroj N and Srivastava S (2019). Higher order assessment of OCT in diabetic macular edema from the VISTA Study: ellipsoid zone dynamics and the retinal fluid index. Ophthalmology Retina. 3(12):1056-1066.

34. Xu B, Song B, Lu X, Kim J, Hu M, Zhao JC and Yu J (2019). Altered chromatin recruitment by FOXA1 mutations promotes androgen independence and prostate cancer progression. Cell Research. 29(9):773-775.

33. Jiang A, Srivasava SK, Figueiredo N, Babiuch A, Hu M, Reese J and Ehlers JP (2019). Repeatability of automated leakage quantification and microaneurysm identification utilizing an analysis platform for ultra-widefield fluorescein angiography. British Journal of Ophthalmology. 104(4):500-503.

32. Uchida A, Hu M, Babiuch A, Srivastava SK, Singh SP, Kaiser PK, Talcott K, Rachitskaya A and Ehlers JP (2019). Optical coherence tomography angiography characteristics of choroidal neovascularization requiring varied dosing frequencies in treat-and-extend management: an analysis of the AVATAR study. PLOS One. 14(6):e0218889.

31. Jiang A, Reese J, Srivastava S, Hach J, Boss J, Lunasco L, Hu M, Babiuch A, Figueiredo N, Le T, Talcott K, Rogozinski A, Sharma S and Ehlers JP (2019). Quantitative ultrawide field angiography and diabetic retinopathy severity: an assessment of panretinal leakage index, ischemic index and microaneurysm count. Ophthalmology. 126(11):1527-1532.

30. Deng X, Wang X, Hu S and Hu M (2019) A general result on complete convergence for weighted sums of linear processes and its statistical applications. Statistics. 53(4):903-920.

29. Yamada T, Yang Y, Valnegri P, Juric I, Abnousi A, Markwalter KY, Guthrie AN, Godec A, Oldenborg A, Hu M, Holy TE and Bonni A. (2019) Sensory experience remodels genome architecture in neural circuit to drive motor learning. Nature. 569(7758):708-713.

28. Babiuch A, Uchida A, Figueiredo N, Hu M, Khan M, Srivastava SK, Singh RP, Rachitskaya A, Kaiser PK, Reese JL and Ehlers JP. (2019) Impact of optical coherence tomograhpy angiography review strategy on detection of choroidal neovascularization. Retina. 40(4):672-678.

27. Ehlers JP, Uchida A, Srivastava SK and Hu M. (2019) Predictive model for macular hole closure speed: insights from intraoperative optical coherence tomography. Translational Vision Science and Technology. 8(1): 18-18.

26. Koshkin V, Garcia J, Reynolds J, Elson P, Magi-Galluzzi C, McKenney J, Isse K, Bishop E, Saunders L, Balyimez A, Rashid S, Hu M, Stephenson A, Fergany A, Lee B, Haber G, Dowlati A, Gilligan T, Ornstein M, Rini B, Mian O and Grivas P. (2019) Transcriptomic and protein analysis of small cell bladder cancer (SCBC) identifies prognostic biomarkers and DLL3 as a relevant therapeutic target. Clinical Cancer Research. 25(1): 210-221.

25. Ugwuegbu O, Uchida A, Singh RP, Beven L, Hu M, Srivastava SK and Ehlers JP. (2019) Quantitative assessment of outer retinal layers and ellipsoid zone mapping in hydroxychloroquine retinopathy. British Journal of Ophthalmology. 103(1): 3-7.

24. Li M, Santpere G, Kawasawa YI, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang H, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, Leeuw CA, Pardinas A, BrainSpan Consortium, PsychENCODE Consortium, PsychENCODE Developmental Subgroup, Hu M, Jin F, Li Y, Owen MJ, O'Donovan MC, Walters JTR, Posthuma D, Levitt P, Weinberger DR, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA and Sestan N. (2018) Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science. 362 (6420), eaat7615.

23. Wang Y, Song F, Zhong B, Zhang L, Xu J, Kuang D, Li D, Choudhary M, Li Y, Hu M, Hardison R, Wang T and Yue F. (2018) The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biology. 19(1): 151.

22. Arepalli S, Srivastava SK, Hu M, Kaiser PM, Dukles N, Reese JL and Ehlers JP. (2018) Assessment of inner and outer retinal layer metrics on the cirrus HD-OCT platform in normal eyes. PLoS One. 13(10):e0203324.

21. Babiuch AS, Khan M, Hu M, Kaiser PK, Srivastava SK, Singh RP, Watts A, Reese JL and Ehlers JP (2018). Comparison of OCT angiography review strategies to identify vascular abnormalities in the AVATAR study. Ophthalmology Retina. 2(6), 606-612

20. Li Y, Hu M and Shen Y. (2018) Gene regulation in the 3D genome. Human Molecular Genetics. 27(R2), R228-R233.

19. Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS Yang J, Zhang F, eQTLGen, 23andMe, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium. (2018) Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nature Genetics. 50(5), 668.

18. Zhang Y, Lin A, Xu J, Zheng JW, Hu M, Tang J and Yue F. (2018) Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus. Nature Communications. 9(1), 750.

17. Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka and Ren B (2018). Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Research. 28(2), 204.

16. Hui D, Fang Z, Lin J, Duan Q, Li Y, Hu M and Chen W. (2017) LAIT: a local ancestry inference toolkit. BMC Genetics. 18(1): 83.

15. Ehlers JP, Wang K, Vasanji A, Hu M and Srivastava SK. (2017) Automated quantitative characterization of retinal vascular leakage and microaneurysms in ultra-widefield fluorescein angiography. British Journal of Ophthalmology. 101: 696-699.

14. Fong K, Zhao JC, Kim J, Li S, Yang YA, Song B, Rittie L, Hu M, Yang X, Perbal B and Yu J. (2017) Polycomb-mediated disruption of an androgen receptor feedback loop derives castration-resistant prostate cancer. Cancer Research. 77(2): 412-422.

13. Qin ZS, Li B, Conneely KN, Wu H, Hu M, Ayyala D, Park Y, Jin VX, Zhang F, Zhang H, Li L and Lin S. (2016) Statistical challenges in analyzing methylation and long-range chromosomal interaction data. Statistics in Biosciences. 1-26.

12. Grudzen CR, Richardson LD, Johnson PN, Hu M, Wang B, Ortiz JM, Kistler EA, Chen A and Morrison RS. (2016) Emergency department-initiated palliative care in advanced cancer: a randomized clinical trial. JAMA oncology, 2(5): 591-598.

11. Smith SW, Jamin CT, Malik S, Abrukin L, Tupchong KM, Portelli I, Asaeda G, Prezant DJ, Wang B, Hu M, Goldfrank LR and Meyers CM. (2016) Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. Disaster Medicine and Public Health Preparedness. 10(3): 496-502.

10. Smith SW, Braun J, Portelli I, Malik S, Asaeda G, Lancet E, Wang B, Hu M, Lee CD, Prezant DJ and Goldfrank LR. (2016) Prehospital indicators for disaster preparedness and response: New York City Emergency Medical Services in Hurricane Sandy (CDC-Sandy). Disaster Medicine and Public Health Preparedness. 10(3): 333-343.

9. Li L, Lyu X, Hou C, Takenaka N, Nguyen HQ, Tong OC, Potts CC, Hu M, Lei EP, Bosco G, Qin ZS and Corces VG. (2015) Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Molecular Cell. 58(2):216-231. Cover image of the April 16, 2015 issue.

8. Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM, Liu JS, Collins JJ, Lerou PH. (2014) The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Reports, 7(1): 70-78. Abstract. Full paper.

7. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS and Ren B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380. Abstract. Full paper. Media.

6. Zhao CJ, Yu J, Runkle C, Wu L, Hu M, Wu D, Liu JS, Wang Q, Qin ZS and Yu J. (2012) Cooperation between polycomb and androgen receptor during oncogenic transformation. Genome Research, 22(2): 322-311. Abstract. Full paper.

5. Zandevakili P, Hu M and Qin ZS. (2012) GPUmotif: An ultra-fast and energy-efficient motif analysis program using graphics processing units. PloS One, 7(5): e36865. Abstract. Full paper. Download software GPUmotif.

4. Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M, Hu M, Sam L, Grasso C, Maher CA, Palanisamy N, Mehra R, Kominsky HD, Siddiqui J, Yu J, Qin ZS and Chinnaiyan AM. (2011) Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Research, 21(7): 1028-1041. Abstract. Full paper.

3. Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J and Chinnaiyan AM. (2010) HPeak: An HMM-based algorithm for de.ning read-enriched regions in ChIP-Seq data. BMC Bioinformatics, 11(1): 369. Abstract. Full paper. Download software HPeak.

2. Yu J, Yu J, Mani RS, Cao Q, Brenner CJ, Cao X, Wang X, Wu L, Li J, Hu M, Gong Y, Cheng H, Laxman B, Vellaichamy A, Shankar S, Li Y, Dhanasekaran SM, Morey R, Barrette T, Lonigro RJ, Tomlins SA, Varambally S, Qin ZS and Chinnaiyan AM. (2010) An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell, 17(5): 443-454. Abstract. Full paper.

1. Hu S and Hu M. (2006) A general approach rate to the strong law of large numbers. Statistics and Probability Letters, 76(8): 843-851.