Computational and Synthetic Biology

Computational and Synthetic Biology

Group Leaders
Group Members

Overview

Our group is interested in applying techniques ranging from modern machine learning and computational structural biology to high-throughput experimental methods such as NGS-based screening, in order to understand how genetic variation affects biological phenotypes (reverse engineering), as well as to design DNA sequences that can generate desired phenotypes (forward engineering). Currently, we are studying how mutations affect heterologous gene expression and transcriptional regulation on microalgae.

Selected Publications

Yang J.S.* Garriga-Canut M.*, Link N., Carolis C., Broadbent K., Beltran-Sastre V., Serrano L., Maurer S.P.#
rec-YnH enables simultaneous many-by-many detection of direct protein-protein and protein-RNA interactions
(2018) Nature Communications, 9(1):3747
(*co-first authors, #co-corresponding authors)

Yus E.*, Yang J.S.*, Sogues A., Serrano L. 
A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants 
(2017) Nature Communications, 8(1):368 

Seo S.W.*, Yang J.S.*, Cho H.S., Yang J., Kim S.C., Park J.M., Kim S., Jung G.Y. 
Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels
(2014) Scientific Reports, 4:4515. 

Seo S.W.*, Yang J.S.*, Kim I., Yang J., Min B.E., Kim S., Jung G.Y. 
Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency  (2013) Metabolic Engineering, 15:67-74

Yang J.S.*, Seo S.W.*, Jang S., Jung G.Y.+, Kim S.+ 
Rational engineering of enzyme allosteric regulation through sequence evolution analysis
(2012) PLoS Computational Biology; 8(7): e1002612

Kim J., Kim I., Yang J.S., Shin Y.E., Hwang J., Park S., Choi Y.S., Kim S.
Rewiring of PDZ domain-ligand interaction network contributed to eukaryotic evolution
(2012) PLoS Genetics, 8(2): e1002510

Park S., Yang J.S., Shin Y.E., Park J., Jang S.K., Kim S.
Protein localization as a principal feature of the etiology and comorbidity of genetic diseases.
(2011) Molecular Systems Biology 7: 494 

Yang J.S., Kim J., Park S., Jeon J., Shin Y.E., Kim S. 
Spatial and functional organization of mitochondrial protein network
(2013) Scientific Reports, 3:1403

Yang J.S., Campagna A., Delgado J., Vanhee P., Serrano L.+, Kiel C.+ 
SAPIN: Structural Analysis for Protein Interaction Networks 
(2012) Bioinformatics 28(22):2998-9

Choi D.S.*, Yang J.S.*, Choi E.J.*, Jang S.C., Park S., Kim O.Y., Hwang D., Kim K.P., Kim Y.K., Kim S+, Gho Y.S.+
The protein interaction network of extracellular vesicles derived from human colorectal cancer cells
(2012) Journal of Proteome Research 11(2):1144-51 

Yang J.S., Nam H.J., Seo M., Han S.K., Choi Y., Nam H.G., Lee S.J., Kim S. 
OASIS: Online Application for the Survival Analysis of Lifespan Assays Performed in Aging Research
(2011) PLoS One; 6(8):e23525

Yang J.S.*, Kim J.T.*, Jeon J., Park H.S., Kang G.H., Park K.S., Lee H.K., Kim S., Cho Y.M.
Changes in hepatic gene expression upon oral administration of taurine-conjugated ursodeoxycholic acid in ob/ob mice. 
(2010) PLoS One, 5(11):e13858