Huiming Ding

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Contact Info

Huiming Ding

Huiming Ding

• BioMicroCenter Building 68-223
• CHISHOLM LAB Building 48-209
• Massachusetts Institute of Technology
• 77 Massachusetts Avenue
• Cambridge, Massachusetts, 02139-4307.
• Email me through OpenWetWare

Education

• PhD, Physics
• BS, Physics

Research interests

1. Proportal Prochlorococcus Portal is a web analytical tool for Prochlorococcus, a model system for Integrative Systems Biology.
2. Galaxy at MIT is a GALAXY INSTANCE installed at MIT.
3. BioMicroWare (BMW) is an integrative experimental and analytical platform specifically developed at MIT to support next generation sequencing technologies.
4. LncRNA Project.
5. Genetic Interaction Network

Calendar

Refer to the Calandar for schedule, status and progress of active projects.

Publications

Serach pubget: http://pubget.com/search?q=authors%3A%22Huiming%20Ding%22

1. Kelly L, Ding H, Huang KH, Osburne MS, and Chisholm SW. Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. ISME J. 2013 Sep;7(9):1827-41. DOI:10.1038/ismej.2013.58 |
2. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, and Boyer LA. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell. 2013 Jan 31;152(3):570-83. DOI:10.1016/j.cell.2013.01.003 |
3. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, and Bruneau BG. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28;151(1):206-20. DOI:10.1016/j.cell.2012.07.035 |
4. Kelly L, Huang KH, Ding H, and Chisholm SW. ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40. DOI:10.1093/nar/gkr1022 |
5. Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, and Emili A. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 2011 Nov;7(11):e1002377. DOI:10.1371/journal.pgen.1002377 |
6. Greenland KB, Ding H, Costanzo M, Boone C, and Davis TN. Identification of Saccharomyces cerevisiae spindle pole body remodeling factors. PLoS One. 2010 Nov 12;5(11):e15426. DOI:10.1371/journal.pone.0015426 |
7. Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, and Myers CL. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods. 2010 Dec;7(12):1017-24. DOI:10.1038/nmeth.1534 |
8. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, and Boone C. The genetic landscape of a cell. Science. 2010 Jan 22;327(5964):425-31. DOI:10.1126/science.1180823 |
9. Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, and Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. DOI:10.1093/nar/gkp820 |
10. Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, and Emili A. eSGA: E. coli synthetic genetic array analysis. Nat Methods. 2008 Sep;5(9):789-95. DOI:10.1038/nmeth.1239 |
11. Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, and Krogan NJ. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007 Apr 12;446(7137):806-10. DOI:10.1038/nature05649 |
12. Davierwala AP, Haynes J, Li Z, Brost RL, Robinson MD, Yu L, Mnaimneh S, Ding H, Zhu H, Chen Y, Cheng X, Brown GW, Boone C, Andrews BJ, and Hughes TR. The synthetic genetic interaction spectrum of essential genes. Nat Genet. 2005 Oct;37(10):1147-52. DOI:10.1038/ng1640 |
13. Measday V, Baetz K, Guzzo J, Yuen K, Kwok T, Sheikh B, Ding H, Ueta R, Hoac T, Cheng B, Pot I, Tong A, Yamaguchi-Iwai Y, Boone C, Hieter P, and Andrews B. Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation. Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13956-61. DOI:10.1073/pnas.0503504102 |
14. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, and Boone C. Global mapping of the yeast genetic interaction network. Science. 2004 Feb 6;303(5659):808-13. DOI:10.1126/science.1091317 |
15. Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, and Boone C. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol. 2004 Jan;22(1):62-9. DOI:10.1038/nbt919 |
16. Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, and Greenblatt JF. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003 Dec;12(6):1565-76. DOI:10.1016/s1097-2765(03)00497-0 |

Useful links

• BioMicroCenter
• Laurie A. Boyer Lab
• CHISHOLM LAB
• Boone Lab

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• DNA Sequencing Research Group (DSRG)

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• Introductory tutorial
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