Education
Ph.D., Computer Science, University of California - Riverside, 2004
Research Interests
Computational Biology and Bioinformatics<br>Statistical Genomics and Personal Genomics<br>Systems Biology<br>Data Mining and Machine Learning
Teaching Interests
Bioinformatics<br>Algorithms<br>Data Mining and Machine Learning
Publications
Chen, H., Cheng, F., & Li, J.
(2020).
iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding.
PLoS Computational Biology,
16
(7).
Zeng, X., Zhu, S., Hou, Y., Zhang, P., Li, L., Li, J., ... Cheng, F.
(2020).
Network-based prediction of drugtarget interactions using an arbitrary-order proximity embedded deep forest.
Bioinformatics,
36
(9),
2805-2812.
Menden, M., Wang, D., Mason, M., Szalai, B., Bulusu, K., Guan, Y., ... Saez-Rodriguez, J.
(2019).
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Nature Communications,
().
Qiao, S., Yan, B., & Li, J.
(2018).
Ensemble learning for protein multiplex subcellular localization prediction based on weighted KNN with different features.
APPLIED INTELLIGENCE,
48
(7),
1813-1824.
Mo, C., Jian, J., Li, J., Fang, Z., Zhao, Z., Yuan, Z., ... Yu, D.
(2018).
Boosting water oxidation on metal-free carbon nanotubes via directional interfacial charge-transfer induced by an adsorbed polyelectrolyte.
ENERGY & ENVIRONMENTAL SCIENCE,
11
(12).
Hayes, M., & Li, J.
(2015).
An integrative framework for the identification of double minute chromosomes using next generation sequencing data.
BMC GENETICS,
16
(),
-.
Wang, Z., Yang, S., Zhang, X., & Li, J.
(2014).
Drug repositioning by integrating target information through a heterogeneous network model..
Bioinformatics (Oxford, England),
30
(20),
2923-30.
Hayes, M., & Li, J.
(2013).
Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data..
BMC bioinformatics,
14 Suppl 5
(),
S6.
Wang, Z., Yin, X., Soo Pyon, Y., Hayes, M., & Li, J.
(2013).
Rare variant discovery and calling by sequencing pooled samples with overlaps..
Bioinformatics (Oxford, England),
29
(1),
29-38.
Li , X., & Li, J.
(2012).
Haplotype inference..
Methods in molecular biology (Clifton, N.J.),
850
(),
411-21.
Li , X., & Li, J.
(2011).
Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference..
Journal of computational biology : a journal of computational molecular cell biology,
18
(11),
1411-21.
Li, J., Horstman, B., & Chen, Q.
(2011).
Detecting epistatic effects in association studies at a genomic level based on an ensemble approach..
Bioinformatics (Oxford, England),
27
(13),
i222-9.
Chen, Q., Wang, Z., Zhou, Y., Shields, R., Chanda, S., Elston, R., ... Li, J.
(2011).
In silico gene prioritization by integrating multiple data sources..
PloS one,
6
(6),
e21137.
Li , X., Yin, X., & Li, J.
(2010).
Efficient identification of identical-by-descent status in pedigrees with many untyped individuals..
Bioinformatics (Oxford, England),
26
(12),
i191-8.
Yin, X., & Li, J.
(2010).
Detecting copy number variations from array CGH data based on a conditional random field model..
Journal of bioinformatics and computational biology,
8
(2),
295-314.
Chen, Q., Li , X., & Li, J.
(2010).
A novel approach for haplotype-based association analysis using family data..
BMC bioinformatics,
11 Suppl 1
(),
S45.
Narayanan, K., & Li, J.
(2010).
MAVEN: a tool for visualization and functional analysis of genome-wide association results..
Bioinformatics (Oxford, England),
26
(2),
270-2.
Li , X., Chen, Q., & Li, J.
(2010).
Detecting genome-wide haplotype polymorphism by combined use of Mendelian constraints and local population structure..
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing,
(),
348-58.
Erten, S., Li , X., Bebek, G., Li, J., & Koyutürk, M.
(2009).
Phylogenetic analysis of modularity in protein interaction networks..
BMC bioinformatics,
10
(),
333.
Li , X., & Li, J.
(2009).
An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions..
Journal of bioinformatics and computational biology,
7
(3),
521-45.
Igo, Jr, R., Li, J., & Goddard, K.
(2009).
Association mapping by generalized linear regression with density-based haplotype clustering..
Genetic epidemiology,
33
(1),
16-26.
Li, J.
(2008).
Prioritize and select SNPs for association studies with multi-stage designs..
Journal of computational biology : a journal of computational molecular cell biology,
15
(3),
241-57.
Li, J., & Jiang, T.
(2008).
A survey on haplotyping algorithms for tightly linked markers..
Journal of bioinformatics and computational biology,
6
(1),
241-59.
Li, J., & Chen, Q.
(2008).
Generating samples for association studies based on HapMap data..
BMC bioinformatics,
9
(),
44.
Li, J.
(2008).
A novel strategy for detecting multiple loci in Genome-Wide Association Studies of complex diseases..
International journal of bioinformatics research and applications,
4
(2),
150-63.
Li , X., & Li, J.
(2008).
Efficient haplotype inference from pedigrees with missing data using linear systems with disjoint-set data structures..
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference,
7
(),
297-308.
Li , X., & Li, J.
(2007).
Comparison of haplotyping methods using families and unrelated individuals on simulated rheumatoid arthritis data..
BMC proceedings,
1 Suppl 1
(),
S55.
Igo, Jr, R., Londono, D., Miller, K., Parrado, A., Quade, S., Sinha, A., ... Goddard, K.
(2007).
Density-based clustering in haplotype analysis for association mapping..
BMC proceedings,
1 Suppl 1
(),
S27.
Li, J.
(2007).
Marker selection for whole-genome association studies with two-stage designs using dense single-nucleotide polymorphisms..
BMC proceedings,
1 Suppl 1
(),
S136.
Li, J., Zhou, Y., & Elston, R.
(2006).
Haplotype-based quantitative trait mapping using a clustering algorithm..
BMC bioinformatics,
7
(),
258.
Li, J., & Jiang, T.
(2005).
Haplotype-based linkage disequilibrium mapping via direct data mining..
Bioinformatics (Oxford, England),
21
(24),
4384-93.
Li, J., & Jiang, T.
(2005).
Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming..
Journal of computational biology : a journal of computational molecular cell biology,
12
(6),
719-39.
