Jing Li

Professor, Computer and Data Sciences Department
Develops computational approaches and software tools for genomics, bioinformatics and systems biology, and creates computational solutions for big data analytics
Office: 509 Olin Phone Number: (216) 368-0356 Email: jingli@case.edu

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., Huang, L., Lewis, S., Nussinov, R., & Cheng, F. (2020). Network-based prediction of drug–target 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., Yu, T., Kang, J., Jeon, M., Wolfinger, R., Nguyen, T., Zaslavskiy, M., Abante, J., Abecassis, B., Aben, N., Aghamirzaie, D., Aittokallio, T., Akhtari, F., Al-lazikani, B., Alam, T., Allam, A., Allen, C., De Almeida, M., Altarawy, D., Alves, V., Amadoz, A., Anchang, B., Antolin, A., Ash, J., Aznar, V., Ba-alawi, W., Bagheri, M., Bajic, V., Ball, G., Ballester, P., Baptista, D., Bare, C., Bateson, M., Bender, A., Bertrand, D., Wijayawardena, B., Boroevich, K., Bosdriesz, E., Bougouffa, S., Bounova, G., Brouwer, T., Bryant, B., Calaza, M., Calderone, A., Calza, S., Capuzzi, S., Carbonell-Caballero, J., Carlin, D., Carter, H., Castagnoli, L., Celebi, R., Cesareni, G., Chang, H., Chen, G., Chen, H., Chen, H., Cheng, L., Chernomoretz, A., Chicco, D., Choi, K., Cho, S., Choi, D., Choi, J., Choi, K., Choi, M., Cock, M., Coker, E., Cortes-Ciriano, I., Cserz\"o, Mikl\'os, I., Cubuk, C., Curtis, C., Daele, D., Dang, C., Dijkstra, T., Dopazo, J., Draghici, S., Drosou, A., Dumontier, M., Ehrhart, F., Eid, F., ElHefnawi, M., Elmarakeby, H., Van Engelen, B., Engin, H., De Esch, I., Evelo, C., Falcao, A., Farag, S., Fernandez-Lozano, C., Fisch, K., Flobak, A., Fornari, C., Foroushani, A., Fotso, D., Fourches, D., Friend, S., Frigessi, A., Gao, X., Gao, X., Gerold, J., Gestraud, P., Ghosh, S., Gillberg, J., Godoy-Lorite, A., Godynyuk, L., Godzik, A., Goldenberg, A., Gomez-Cabrero, D., Gonen, M., De Graaf, C., Gray, H., Grechkin, M., Guimera, R., Guney, E., Haibe-Kains, B., Han, Y., Hase, T., Bagheri-Hamaneh, M., He, L., Heath, L., Hellton, K., Helmer-Citterich, M., Hidalgo, M., Hidru, D., Hill, S., Hochreiter, S., Hong, S., Hovig, E., Hsueh, Y., Hu, Z., Huang, J., Huang, R., Hunyady, L\'aszl\'o, R., Hwang, J., Hwang, T., Hwang, W., Hwang, Y., Isayev, O., Don't Walk, O., Jack, J., Jahandideh, S., Ji, J., Jo, Y., Kamola, P., Kanev, G., Karacosta, L., Karimi, M., Kaski, S., Kazanov, M., Khamis, A., Khan, S., Kiani, N., Kim, A., Kim, J., Kim, J., Kim, K., Kim, K., Kim, S., Kim, Y., Kim, Y., Kirk, P., Kitano, H., Klambauer, G., Knowles, D., Ko, M., Kohn-Luque, A., Kooistra, A., Kuenemann, M., Kuiper, M., Kurz, C., Kwon, M., Van Laarhoven, T., Laegreid, A., Lederer, S., Lee, H., Lee, E., Lee, J., Lepp\_aho, Eemeli, J., Lewis, R., Li, J., Li, L., Liley, J., Lim, W., Lin, C., Liu, Y., Lopez, Y., Low, J., Lysenko, A., Machado, D., Madhukar, N., Maeyer, D., Malpartida, A., Mamitsuka, H., Marabita, F., Marchal, K., Marttinen, P., Mason, D., Mazaheri, A., Mehmood, A., Mehreen, A., Michaut, M., Miller, R., Mitsopoulos, C., Modos, D., Moerbeke, M., Moo, K., Motsinger-Reif, A., Movva, R., Muraru, S., Muratov, E., Mushthofa, M., Nagarajan, N., Nakken, S., Nath, A., Neuvial, P., Newton, R., Ning, Z., Niz, C., Oliva, B., Olsen, C., Palmeri, A., Panesar, B., Papadopoulos, S., Park, J., Park, S., Park, S., Pawitan, Y., Peluso, D., Pendyala, S., Peng, J., Perfetto, L., Pirro, S., Plevritis, S., Politi, R., Poon, H., Porta, E., Prellner, I., Preuer, K., Pujana, M., Ramnarine, R., Reid, J., Reyal, F., Richardson, S., Ricketts, C., Rieswijk, L., Rocha, M., Rodriguez-Gonzalvez, C., Roell, K., Rotroff, D., De Ruiter, J., Rukawa, P., Sadacca, B., Safikhani, Z., Safitri, F., Sales-Pardo, M., Sauer, S., Schlichting, M., Seoane, J., Serra, J., Shang, M., Sharma, A., Sharma, H., Shen, Y., Shiga, M., Shin, M., Shkedy, Z., Shopsowitz, K., Sinai, S., Skola, D., Smirnov, P., Soerensen, I., Soerensen, P., Song, J., Song, S., Soufan, O., Spitzmueller, A., Steipe, B., Suphavilai, C., Tamayo, S., Tamborero, D., Tang, J., Tanoli, Z., Tarres-Deulofeu, M., Tegner, J., Thommesen, L., Tonekaboni, S., Tran, H., Troyer, E., Truong, A., Tsunoda, T., Turu, G\'abor, T., Tzeng, G., Verbeke, L., Videla, S., Vis, D., Voronkov, A., Votis, K., Wang, A., Wang, H., Wangkawee, K., Wang, S., Wang, Z., Wang, X., Wang, X., Wennerberg, K., Wernisch, L., Wessels, L., Van Westen, G., Westerman, B., White, S., Willighagen, E., Wurdinger, T., Xie, L., Xie, S., Xue, Y., Yadav, B., Yau, C., Yeerna, H., Yin, J., Yu, M., Yu, M., Yun, S., Zakharov, A., Zamichos, A., Zanin, M., Zeng, L., Zenil, H., Zhang, F., Zhang, P., Zhang, J., Zhao, H., Zhao, L., Zheng, W., Zoufir, A., Zucknick, M., Jang, I., Ghazoui, Z., Ahsen, M., Vogel, R., Neto, E., Norman, T., Tang, E., Garnett, M., Veroli, G., Fawell, S., Stolovitzky, G., Guinney, J., Dry, J., & Saez-Rodriguez, J. (2019). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications.
Mo, C., Jian, J., Li, J., Fang, Z., Zhao, Z., Yuan, Z., Yang, M., Zhang, Y., Dai, L., & 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).
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.
Qiao, S., Yan, B., & Li, J. (2017). Ensemble learning for protein multiplex subcellular localization prediction based on weighted KNN with different features. Applied Intelligence.
Wu, Y., Jin, R., Li, J., & Zhang, X. (2015). Robust Local Community Detection: On Free Rider Effect and Its Elimination. Proc. VLDB Endow., 8 (7), 798–809.
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.
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.
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.
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.
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., Kim, S., Wongkasemjit, S., Li, J., & 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.