Ya-Fan Chan, Pei-Wen Chiang, Kshitij Tandon, Denis Rogozin, Andrey Degermendzhi. Vladimir Zykov, and Sen-Lin Tang, Spatiotemporal Changes in the Bacterial Community of the Meromictic Lake Uchum, Siberia. Microb Ecol (2020). Available from:https://doi.org/10.1007/s00248-020-01592-92019
Justin Chan, Kazuhiro Takemura, Hong-Rui Lin, Kai-Chun Chang, Yuan-Yu Chang, Yasumasa Joti, Akio Kitao* and Lee-Wei Yang*. An Efficient Timer and Sizer of Biomacromolecular Motions. Structure 2019. Accepted for publication.
Justin Chan, Jinhao Zou, Christopher Llynard Ortiz, Chi-Hong Chang Chien, Rong-Long Pan, Lee-Wei Yang*. DR-SIP: Protocols for Higher Order Structure Modeling with Distance Restraints- and Cyclic Symmetry-Imposed Packing. Bioinformatics. 2019. doi:10.1093/bioinformatics/btz579 <
Haoyu Cheng, Wai Soon Chan, Zhixiu Li, Dan Wang, Song Liu,* and Yaoqi Zhou*. Small Open Reading Frames: Current Prediction Techniques and Future Prospect. Curr Protein Pept Sci. 2011;12(6):503-507. doi:10.2174/138920311796957667.
"Metagenomic, phylogenetic, and functional
characterization of predominant endolithic
green sulfur bacteria in the coral Isopora
palifera",
Microbiome, 7:3,
4
January
2019.
Ching-Ching Yeh, Jun-Liang Luo,
Nam Nhut Phan, Yi-Chun
Cheng, Lu-Ping Chow, Mong-Hsun Tsai,
Eric Y. Chuang and Liang-Chuan Lai,
"Different effects of long noncoding RNA
NDRG1-OT1 fragments on NDRG1
transcription in breast cancer cells
under hypoxia", RNA Biology, 04
December 2018.
Available from:
https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1553480?scroll=top&needAccess=true
Salawu, E. O.* In
Silico Study Reveals How E64 Approaches,
Binds to, and Inhibits Falcipain-2 of
Plasmodium falciparum that Causes
Malaria in Humans. Sci. Rep. 2018, 8,
34622. Available from
https://doi.org/10.1038/s41598-018-34622-1.
(2017 IF: 4.1; 5-yr IF 4.6)
Neha Warikoo,
Yung-Chun Chang, Wen-Lian Hsu;
"LPTK: a
linguistic pattern-aware dependency tree
kernel approach for the BioCreative VI
CHEMPROT task,"
Database, Volume 2018, 1 January
2018, bay108,
https://doi.org/10.1093/database/bay108
Neha
Warikoo,
Yung-Chun
Chang,
Hong-Jie
Dai,
and
Wen-Lian
Hsu,
"An Ensemble
Neural Network Model for Benefiting
Pregnancy Health Stats from Mining
Social Media," to appear in
The Asia Information Retrieval Societies
Conference 2018.
Joanito, I., Chu J.-W., Wu
S.H. and Hsu C.-P., An incoherent feed-forward
loop switches the Arabidopsis clock rapidly
between two hysteretic states. Scientific
Reports, 2018. 8(1): p.
13944. doi: 10.1038/s41598-018-32030-z
Salawu, E. O.*.
The Impairment of TorsinA’s Binding to and
Interactions with Its Activator: An Atomistic
Molecular Dynamics Study of Primary Dystonia.
Front. Mol. Biosci.2018,
5. Available from:
https://doi.org/10.3389/fmolb.2018.00064.
Wu J.-F., Tsai H.-L., Joanito I.,
Wu Y.-C., Chang C.-W., Li Y.-H., Wang Y.,
Hong J. C., Chu J.-W., Hsu C.-P., and Wu
S.-H. LWD-TCP complex activates the morning
gene CCA1 in Arabidopsis. Nature
Communications, 2016.
7: p. 13181. doi: 10.1038/ncomms13181
Chen, W.-T.; Huang, W.-Y.; Chen, T.; Salawu, E.
O.; Wang, D.; Lee, Y.-Z.; Chang, Y.-Y.; Yang,
L.-W.; Sue, S.-C.; Wang, X.; Yin H-S*. Structure and
Function of Chicken Interleukin-1 Beta Mutants:
Uncoupling of Receptor Binding and in Vivo
Biological Activity. Sci. Rep.2016,
6, 27729. Available
from: https://doi.org/10.1038/srep27729. (2017
IF: 4.1; 5-yr IF 4.6)
Salawu, E. O.* RaFoSA: Random Forests Secondary Structure
Assignment for Coarse-Grained and All-Atom Protein
Systems. Cogent Biol.2016, 2
(1), 1214061. Available from: https://doi.org/10.1080/23312025.2016.1214061.
Priori, D.*; de Sousa, G.; Roisenberg, M.;
Stopford, C.; Hesse, E.; Salawu, E. O.;
Davey, N.; Sun, Y.
Using Machine Learning Techniques to Recover
Prismatic Cirrus Ice Crystal Size from
2-Dimensional Light Scattering Patterns. In
International Conference on Artificial
Neural Networks;
2016;
pp 372–379. Available
from:https://link.springer.com/chapter/10.1007/978-3-319-44781-0_44.
Bernhard Schaefke, Tzi-Yuan Wang, Chuen-Yi Wang, Wen-Hsiung
Li. "Gains and losses of
Transcription Factor Binding Sites in Saccharomyces
cerevisiae and S. paradoxus"
Accepted for publication by
: Genome Biology and Evolution
Ching-Hung Tseng, Pei-Wen Chiang,
Hung-Chung Lai, Fuh-Kwo Shiah, Ting-Chang Hsu, Yi-Lung
Cheng, Liang-Saw Wen, Chun-Mao Tseng, Wung-Yang Shieh, Isaam
saeed, Saman Halgamuge and Sen-Lin Tang.
"Prokaryotic
assemblages and metagenomes in pelagic zones of the South
China Sea,"BMC
Genomics2015,16:219 doi:10.1186/s12864-015-1434-3
2014
Barh, D.; Chaitankar, V.; Yiannakopoulou, E.
C.; Salawu, E. O.; Chowbina, S.;
Ghosh, P.; Azevedo, V. In Silico Models:
From Simple Networks to Complex Diseases. In
Animal Biotechnology; Elsevier, 2014;
pp 385–404. Available from: https://doi.org/10.1016/B978-0-12-416002-6.00021-3.
Ching-Hung Tseng and Sen-Li
Tang.
"Marine Microbial
Metagenomics: From Individual to the Environment"
Int. J. Mol. Sci.2014,15(5),
8878-8892; doi:10.3390/ijms15058878
Peng, H.-P., K. H. Lee, J.-W. Jian
and A.-S. Yang.
"Origins of specificity and affinity in
antibody–protein
interactions."Proceedings of the National Academy
of Sciences, doi:10.1073/pnas.1401131111, June, 2014.
Khong-Loon Tiong, Kuo-Ching Chang,
Kun-Tu Yeh, Ting-Yuan Liu, Jia-Hong
Wu, Ping-Heng Hsieh, Shu-Hui Lin,
Wei-Yun Lai, Yu-Chin Hsu, Jeou-Yuan
Chen, Jan-Gowth Chang, Grace S.
Shieh.
"CSNK1E/CTNNB1
Are Synthetic Lethal To TP53 in
Colorectal Cancer and Are Markers
for Prognosis."Neoplasia,
doi:10.1016/j.neo.2014.04.007.
Volume 16, Issue 5,
May 2014
Tien WS, Chen YT, Wu KP. "SecretePipe: a screening
pipeline for secreted proteins with competence to
identify potential membrane-bound shed markers." J
Proteome Res. 2013 Mar 1;12(3):1235-44. doi: 10.1021/pr3009012.
Schaefke, B., J. J.
Emerson, T. Y. Wang, M. Y. Lu, L. C. Hsieh and W. H. Li
(2013).
"Inheritance of gene expression level and selective
constraints on trans- and cis-regulatory changes in yeast."Mol Biol Evol.(2013)
doi:
10.1093/molbev/mst114First
published online:
June 22, 2013
Ching-Hung Tseng1,2,3,Pei-Wen
Chiang3,
Fuh-Kwo Shiah4,
Yi-Lung Chen4,
Jia-Rong Liou4,
Ting-Chang Hsu4,
Suhinthan Maheswararajah5,
Isaam Saeed5,
Saman Halgamuge5and
Sen-Lin Tang1,3
"Microbial and viral metagenomes of a subtropical
freshwater reservoir subject to climatic disturbances,"The
ISME Journal(2013)7,2374–2386;
doi:10.1038/ismej.2013.118; published online 11 July 2013
Tien WS, Chen YT, Wu KP. "SecretePipe:
a screening pipeline for secreted proteins with competence
to identify potential membrane-bound shed markers."J Proteome Res. 2013 Mar 1;12(3):1235-44. doi:
10.1021/pr3009012.
C.-H. Hsu, Chien-Kuo Chen, and Ming-Jing Hwang
"The architectural design of networks of protein domain architectures"
Biol. Lett.. 2013; doi:10.1098/rsbl.2013.0268
2012
Lai EY, Wang WB, Jiang T, Wu KP.
"A linear-time algorithm for
reconstructing zero-recombinant haplotype configuration on a
pedigree."BMC Bioinformatics.
2012;13 Suppl 17:S19. doi: 10.1186/1471-2105-13-S17-S19.
Chiang, S., Swamy, B.S. K., Hsu, T.W., Tsai, Z. T.Y., Lu, H.S., Wang, D., and Tsai, H.K.*,
"Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast,"
Gene, volume 491, pages 237-245, January 2012.
Lin KT, Wang YW, Chen CT, Ho CM, Su WH, Jou YS.
"HDAC inhibitors augmented cell migration and metastasis through induction of PKCs leading to identification of low toxicity modalities for combination cancer therapy."Clinical Cancer Res. 2012 Sep 1;18(17):4691-701. (SCI: Impact factor: 7.837, 12/196 ONCOLOGY)
Chang CY, Lin SC, Su WH, Ho CM, Jou YS.
"Somatic LMCD1 mutations promoted cell migration and tumor metastasis in hepatocellular carcinoma."
Oncogene 2012, May 24; 31(21):2640-52. (SCI: Impact factor: 7.357, 19/196 ONCOLOGY)
Kao S, Shiau CK, Gu DL, Ho CM, Su WH, Chen CF, Lin CH, Jou YS. IGDB.NSCLC:
Integrated Genomic Database of Non-Small Cell Lung Cancer,
Nucleic Acids Res. 2012 Jan; 40:D972-D977 (SCI: Impact factor: 8.278, 27/290 BIOCHEMISTRY & MOLECULAR BIOLOGY)
Lin YC, Hsiao CL, Hsieh AR, Lian IeB, Fann CS.
"Using maximal segmental score in genome-wide association studies." Genet Epidemiol.
2012 Sep;36(6):594-601.
Yu, C.-M., H.-P. Peng, I.-C. Chen,
Y.-C. Lee, J.-B. Chen, K.-C. Tsai, C.-T. Chen, J.-Y. Chang,
E.-W. Yang, P.-C. Hsu, J.-W. Jian, H.-J. Hsu, H.-J. Chang,
W.-L. Hsu, K.-F. Huang, A. C. Ma and A.-S. Yang."Rationalization
and Design of the Complementarity Determining Region
Sequences in an Antibody-Antigen Recognition Interface."
PLoS ONE7(3): e33340, March, 2012.
Tsai, Z. T.Y., Huang, G. T.W., and Tsai, H.K.*,
"Simultaneous identification for synergistic transcription factors and their transcription factor binding sites,"
The Fourth International Workshop on Intelligent Informatics in Biology and Medicine (IIBM 2011), June 2011.
Yang, H.-C., Huang, M.-C., Li, L.-H., Lin, C.-H.,
Yu, L. T., Diccianni, M. B., Wu, J.-Y., Chen, Y.-T. and Fann,
C. S. J.
"MPDA: microarray-based
pooled DNA analyzer."BMC Bioinformatics