Ming  Hu,  PhD

Ming Hu, PhD

Assistant Staff

Lerner Research Institute, 9500 Euclid Avenue, Cleveland, Ohio 44195
Location: NE5-262
Email: hum@ccf.org
Phone: (216) 445-5057

Hu Laboratory

 


My research interests lie in the development the statistical methods and computation tools, and their applications to genetic and epigenetic studies. My recent work focuses on genome-wide mapping and analysis of chromosome architecture. Currently, I am a sub-contract PI of the NIH 4D Nucleome consortium grant U54DK107977 (PI: Ren), and lead the development of novel analysis tools to interrogate Hi-C, capture Hi-C, PLAC-Seq and HiChIP data sets. In particular, 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 recent 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). Most recently, I have developed MAPS, a model-based method to identify long-range chromatin interactions from PLAC-Seq and HiChIP experiments (Juric et al, in press, PLOS Computational Biology, 2019). I have also developed methods for analyzing ChIP-Seq data, RNA-Seq data and single cell RNA-Seq data. As a biostatistician, I have contributed to multiple clinical studies in the area of emergency medicine and ophthalmology.

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Bold lists Hu lab members.

57. Ehlers JP, Uchida A, Hu MFigueiredo 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. In press. Ophthalmology Retina.

56. 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. In press. Cell Research. 

55. Jiang A, Srivasava SK, Figueiredo N, Babiuch A, Hu M, Resse J and Ehlers JP (2019). Repeatability of automated leakage quantification and microaneurysm identification utilizing an analysis platform for ultra-widefield fluorescein angiography. In press. British Journal of Ophthalmology.

54. 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 doseing frequencies in treat-and-extend management: an analysis of the AVATAR study. In press. PLOS One.

53. 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 ultra-widefield angiography and diabetic retinopathy severity: an assessment of panretinal leakage index, ischemic index and microaneurysm count. In press. Ophthalmology.

52. 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. In press. Statistics.

51. 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. In press. BMC Genetics. *Co-corresponding author.

50. 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. In press. Nature.

49. Juric I*, Yu M*, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu 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. In press. PLOS Computational Biology. *Co-first author. #Co-corresponding author.

48. 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. In press. Nature Communications. *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.

47. 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. In press. Retina.

46. 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.

45. 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.

44. 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.

43. 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.

42. 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.

41. 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.

40. 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. *Co-corresponding author. In press. IEEE/ACM Transactions on Computational Biology and Bioinformatics.

39. Figueiredo NAL, Srivastava S, Singh RP, Rachitskaya AV, Hu M, Reese J, Stiegel L, Dukles N, Hach J, Lunasco L, Calabrise C, Zhou E and Ehlers JP. (2018) Anatomic feature dynamics and perfusion density following aflibercept therapy in retinal vascular disease in the PERMEATE study. Investigative Ophthalmology & Visual Science. 59(9), 3596-3596.

38. 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

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

36. Wray NR, Ripke S, Mattheisen M, Trazskowski M, ..., Hu M, ..., Lewis CM, Levinson DF, Breen G, Borglum AD, Sullivan PF, eQTLGen consortium, 23andMe research team and the major depression 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.

35. Zhang Y, Lin A, Xu J, Zheng JW, Hu M, Tang J and Yue F. (2018) HiCPlus: a deep convolutional neural network for Hi-C interaction matrix enhancement. Nature Communications. 9(1), 750.

34. 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.

33. Jaber R, Goshe J, Publications Wagenberg S, Hu M, Srivastava SK, Resse J and Ehlers JP. (2017) Comparative outcome assessment of descemet membrane endothelial keratoplasty with and without intraoperative optical coherence tomography guidance from the DISCOVER study. Investigative Ophthalmology & Visual Science. 58(8), 5668-5668.

32. Venkat A, Singh RP, Eisengart J, Hu M, Ehlers JP and Babiuch A. (2017) Neovascular glaucoma management: practice patterns of glaucoma and retina specialists in the United States. Investigative Ophthalmology & Visual Science. 58(8), 3668-3668.

31. Babiuch A, Khan M, Hu M, Kaiser PK, Srivastava SK, Signh RP, Watts A, Reese J and Ehlers JP. (2017) Comparative evaluation of review strategies for detection of vascular abnormalities on optical coherence tomography angiography in the AVATAR Study. Investigative Ophthalmology & Visual Science. 58(8), 1888-1888.

30. Wang K, Srivastava SK, Vasanji A, Hu M, Reese J, Stiegel L and Ehlers JP (2017). Quantitative ultra-widefield fluorescein angiography and volumetric optical coherence tomography analysis in the REACT Study: a prospective randomized comparative dosage trial evaluating ranibizumab in bevacizumab-resistant diabetic macular edema. Investigative Ophthalmology & Visual Science. 58(8), 936-936.

29. 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. *Co-corresponding author. Bioinformatics. 34(1): 139-146.

28. 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.

27. Martin J, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, Hu M* and Li Y* (2017) Hugin: an integrative genome browser for visualizing a compendium of Hi-C data, annotating and detecting potential target genes for GWAS variants. *Co-corresponding author. Bioinformatics. 33(23): 3793-3795.

26. 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.

25. 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.

24. 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.

23. 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. 

22. 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. 

21. 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.

20. 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. 

19. 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.

18. 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.

17. 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.

16. 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.

15. 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.

14. 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. 

13. 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. Featured cover image for this issue in Quantitative Biology. Selected as one of the two featured articles for this issue in Quantitative Biology.

12. 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. 

11. 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. 

10. 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. 

9. 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. 

8. 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. 

7. 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. 

6. 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. 

5. 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 defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics, 11(1): 369. 

4. 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. 

3. 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.

2. 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. 

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.


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