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Qiangfeng Zhang

Qiangfeng Zhang



Research Area:

Our laboratory works in the interface of structural biology, genomics, machine learning and big data analysis. Our main research interest is to develop enabling techniques that combines computational and high throughput experimental investigations for the emerging area of structural systems biology:

1. measure structures of macromolecules (e.g., protein, RNAs, DNAs). In particular, we use high throughput deep sequencing to probe RNA secondary structures.

2. understand structure-function relationship of macromolecules. In particular, we develop effective methods to identify and predict protein functional sites and RNA structural motifs.

3. reconstruct macromolecule (e.g., protein-protein, RNA-RNA, and protein-RNA) interaction networks by using high throughput experimentation and structural modeling;

4. identify genetic mutations that cause disease through structure aberration and network dysregulation, and develop methods for precise diagnosis, prognosis and viable treatment by bridging structures and networks.


Selected Publications:

1.   Spitale R*, Flynn RA*, Zhang QC*, Pete Crisalli, Byron Lee, Jong-Wha Jung, Hannes Y. Kuchelmeister, Pedro J. Batista, Eduardo A. Torre, Eric T. Kool, and Chang HY. Structural imprints in vivo decode mechanisms of RNA regulation. (2015) Nature. In press.

2.   Chu C, Zhang QC, Texira S, Bharadwaj M, Calabrese M, Magnuson T, Heard H and Chang HY. Developmentally regulated and modular assembly of Xist RNA binding proteins coordinate chromatin silencing. (2015) Cell. Accepted.

3.   Wan Y*, Qu K*, Zhang QC, Manor O, Ouyang Z, Zhang J, Snyder MP, Segal E and Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. (2014) Nature, 505 (7485), 706-709.

4.   Kasowski M*, Kyriazopoulou-Panagiotopoulou S*, Grubert F*, Zaugg JB*, Kundaje A*, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive Variation in Chromatin States Across Human Individuals and Populations. (2013)Science 342 (6159), 750-752.

5.   Zhang QC, Petrey D, Garzon J, Deng L, and Honig B. PrePPI: A structure-informed database of protein-protein interactions. (2013) Nucleic Acids Research, 41:D828-33.

6.   Zhang QC*, Petrey D*, Deng L, Qiang L, Shi Y, Chan AT, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, and Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. (2012) Nature, 490: 556-560. Highlighted by Nature Structural & Molecular Biology 19, 1067: A PrePPI way to make predictions; Nature Methods 9, 1139: Predicting PPIs; Recommended by Faculty of 1000 Prime,http://f1000.com/prime/717959331.

7.   Zhang QC*, Deng L*, Guan J, Honig B and Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. (2011) Nucleic Acids Research, 39: W283-87.

8.   Zhang QC, Petrey D, Norel R, and Honig B, Protein interface conservation across structural space. (2010) Proceedings of the National Academy of Sciences, 107(24): 10896-109.  Recommended by Faculty of 1000 prime, http://f1000.com/3534956.

(* Co-first authorship)



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