• 1460 Citations
  • 19 h-Index
20072020

Research output per year

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Research Output

  • 1460 Citations
  • 19 h-Index
  • 27 Article
  • 7 Conference contribution
  • 1 Chapter
  • 1 Comment/debate

A heterogeneous label propagation algorithm for disease gene discovery

Hwang, T. & Kuang, R., 2010, Proceedings of the 10th SIAM International Conference on Data Mining, SDM 2010. p. 583-594 12 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

41 Scopus citations

A hypergraph-based learning algorithm for classifying arraycgh data with spatial prior

Tian, Z., Hwang, T. & Kuang, R., Oct 2 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 5174345. (2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge

Tian, Z., Hwang, T. & Kuang, R., Nov 9 2009, In : Bioinformatics. 25, 21, p. 2831-2838 8 p.

Research output: Contribution to journalArticle

52 Scopus citations

Androgen receptor splice variants mediate enzalutamide resistance in castration-resistant prostate cancer cell lines

Li, Y., Chan, S. C., Brand, L. J., Hwang, T. H., Silverstein, K. A. T. & Dehm, S. M., Jan 15 2013, In : Cancer research. 73, 2, p. 483-489 7 p.

Research output: Contribution to journalArticle

382 Scopus citations

An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types

Park, S., Kim, S. J., Yu, D., Peña-Llopis, S., Gao, J., Park, J. S., Chen, B., Norris, J., Wang, X., Chen, M., Kim, M., Yong, J., Wardak, Z., Choe, K., Story, M., Starr, T., Cheong, J. H. & Hwang, T. H., Jun 1 2016, In : Bioinformatics. 32, 11, p. 1643-1651 9 p.

Research output: Contribution to journalArticle

13 Scopus citations

AR intragenic deletions linked to androgen receptor splice variant expression and activity in models of prostate cancer progression

Li, Y., Hwang, T. H., Oseth, L. A., Hauge, A., Vessella, R. L., Schmechel, S. C., Hirsch, B., Beckman, K. B., Silverstein, K. A. & Dehm, S. M., Nov 8 2012, In : Oncogene. 31, 45, p. 4759-4767 9 p.

Research output: Contribution to journalArticle

137 Scopus citations

Bioinformatics data analysis of next-generation sequencing data from heterogeneous tumor samples

Landman, S. R. & Hwang, T. H., 2017, Methods in Molecular Biology. Humana Press Inc., Vol. 1633. p. 185-192 8 p. (Methods in Molecular Biology; vol. 1633).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chemistry-First Approach for Nomination of Personalized Treatment in Lung Cancer

McMillan, E. A., Ryu, M. J., Diep, C. H., Mendiratta, S., Clemenceau, J. R., Vaden, R. M., Kim, J. H., Motoyaji, T., Covington, K. R., Peyton, M., Huffman, K., Wu, X., Girard, L., Sung, Y., Chen, P. H., Mallipeddi, P. L., Lee, J. Y., Hanson, J., Voruganti, S., Yu, Y. & 20 others, Park, S., Sudderth, J., DeSevo, C., Muzny, D. M., Doddapaneni, H. V., Gazdar, A., Gibbs, R. A., Hwang, T. H., Heymach, J. V., Wistuba, I., Coombes, K. R., Williams, N. S., Wheeler, D. A., MacMillan, J. B., Deberardinis, R. J., Roth, M. G., Posner, B. A., Minna, J. D., Kim, H. S. & White, M. A., May 3 2018, In : Cell. 173, 4, p. 864-878.e29

Research output: Contribution to journalArticle

20 Scopus citations

Co-clustering phenome-genome for phenotype classification and disease gene discovery

Hwang, T., Atluri, G., Xie, M., Dey, S., Hong, C., Kumar, V. & Kuang, R., Oct 1 2012, In : Nucleic acids research. 40, 19, p. e146

Research output: Contribution to journalArticle

42 Scopus citations

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combination DREAM Consortium, Dec 1 2019, In : Nature communications. 10, 1, 2674.

Research output: Contribution to journalArticle

Open Access
18 Scopus citations

Comprehensive ex vivo transposon mutagenesis identifies genes that promote growth factor independence and leukemogenesis

Guo, Y., Updegraff, B. L., Park, S., Durakoglugil, D., Cruz, V. H., Maddux, S., Hwang, T. H. & O'Donnell-Mendell, K. A., Feb 15 2016, In : Cancer Research. 76, 4, p. 773-786 14 p.

Research output: Contribution to journalArticle

11 Scopus citations

Convex optimization for binary classifier aggregation in multiclass problems

Park, S., Hwang, T. H. & Choi, S., 2014, SIAM International Conference on Data Mining 2014, SDM 2014. Society for Industrial and Applied Mathematics Publications, Vol. 1. p. 280-288 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Diverse AR gene rearrangements mediate resistance to androgen receptor inhibitors in metastatic prostate cancer

Li, Y., Yang, R., Henzler, C. M., Ho, Y., Passow, C., Auch, B., Carreira, S., Rodrigues, D. N., Bertan, C., Hwang, T. H., Quigley, D. A., Dang, H. X., Morrissey, C., Fraser, M., Plymate, S. R., PlymateMaher, C. A., Feng, F. Y., De Bono, J. S. & Dehm, S. M., Apr 15 2020, In : Clinical Cancer Research. 26, 8, p. 1965-1976 12 p.

Research output: Contribution to journalArticle

Open Access

DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

Nanavaty, V., Abrash, E. W., Hong, C., Park, S., Fink, E. E., Li, Z., Sweet, T. J., Bhasin, J. M., Singuri, S., Lee, B. H., Hwang, T. H. & Ting, A. H., May 21 2020, In : Molecular cell. 78, 4, p. 752-764.e6

Research output: Contribution to journalArticle

Erratum: Reconstructing Disease Phenome-genome Association by Bi-Random Walk (Bioinformatics (2012))

Xie, M., Hwang, T. & Kuang, R., Aug 15 2014, In : Bioinformatics. 30, 16, 1 p.

Research output: Contribution to journalComment/debate

Inferring disease and gene set associations with rank coherence in networks

Hwang, T., Zhang, W., Xie, M., Liu, J. & Kuang, R., Oct 1 2011, In : Bioinformatics. 27, 19, p. 2692-2699 8 p., btr463.

Research output: Contribution to journalArticle

30 Scopus citations

Inhibition of discoidin domain receptor 1 reduces collagen-mediated tumorigenicity in pancreatic ductal adenocarcinoma

Aguilera, K. Y., Huang, H., Du, W., Hagopian, M. M., Wang, Z., Hinz, S., Hwang, T. H., Wang, H., Fleming, J. B., Castrillon, D. H., Ren, X., Ding, K. & Brekken, R. A., Nov 1 2017, In : Molecular Cancer Therapeutics. 16, 11, p. 2473-2485 13 p.

Research output: Contribution to journalArticle

22 Scopus citations

Integrated omics-analysis reveals Wnt-mediated NAD+ metabolic reprogramming in cancer stem-like cells

Lee, J., Kee, H. J., Min, S., Park, K. C., Park, S., Hwang, T. H., Ryu, D. H., Hwang, G. S. & Cheong, J. H., Jan 1 2016, In : Oncotarget. 7, 30, p. 48562-48576 15 p.

Research output: Contribution to journalArticle

5 Scopus citations

Intersection of DNA privacy and whole-genome sequencing

Changjin, H., Jason, W., Chao, X., Tae, H. H. & Park, J. Y., Jul 1 2015, In : Clinical Chemistry. 61, 7, p. 900-902 3 p.

Research output: Contribution to journalArticle

1 Scopus citations

Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers

Hwang, T. H., Atluri, G., Kuang, R., Kumar, V., Starr, T., Silverstein, K. A. T., Haverty, P. M., Zhang, Z. & Liu, J., Jan 1 2013, In : BMC Genomics. 14, 1, 440.

Research output: Contribution to journalArticle

20 Scopus citations

Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction

Hwang, T., Tian, Z., Kuang, R. & Kocher, J. P., Dec 1 2008, Proceedings - 8th IEEE International Conference on Data Mining, ICDM 2008. p. 293-302 10 p. 4781124. (Proceedings - IEEE International Conference on Data Mining, ICDM).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

23 Scopus citations

MCTA: Target tracking algorithm based on minimal contour in wireless sensor networks

Jeong, J., Hwang, T., He, T. & Du, D., Sep 4 2007, Proceedings - IEEE INFOCOM 2007: 26th IEEE International Conference on Computer Communications. p. 2371-2375 5 p. 4215865. (Proceedings - IEEE INFOCOM).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

59 Scopus citations

MRNA 3′-UTR shortening is a molecular signature of mTORC1 activation

Chang, J. W., Zhang, W., Yeh, H. S., De Jong, E. P., Jun, S., Kim, K. H., Bae, S. S., Beckman, K., Hwang, T. H., Kim, K. S., Kim, D. H., Griffin, T. J., Kuang, R. & Yong, J., Jun 15 2015, In : Nature Communications. 6, 7218.

Research output: Contribution to journalArticle

18 Scopus citations

Network-based phenome-genome association prediction by bi-random walk

Xie, M., Xu, Y., Zhang, Y., Hwang, T. & Kuang, R., May 1 2015, In : PLoS One. 10, 5, e0125138.

Research output: Contribution to journalArticle

17 Scopus citations

Prioritizing disease genes by bi-random walk

Xie, M., Hwang, T. & Kuang, R., May 29 2012, Advances in Knowledge Discovery and Data Mining - 16th Pacific-Asia Conference, PAKDD 2012, Proceedings. PART 2 ed. p. 292-303 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7301 LNAI, no. PART 2).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

25 Scopus citations

PROTOCADHERIN 7 acts through SET and PP2A to potentiate MAPK signaling by EGFR and KRAS during lung tumorigenesis

Zhou, X., Updegraff, B. L., Guo, Y., Peyton, M., Girard, L., Larsen, J. E., Xie, X-J., Zhou, Y., Hwang, T. H., Xie, Y., Rodriguez-Canales, J., Villalobos, P., Behrens, C., Wistuba, I. I., Minna, J. D. & O'Donnell-Mendell, K. A., Jan 1 2017, In : Cancer research. 77, 1, p. 187-197 11 p.

Research output: Contribution to journalArticle

17 Scopus citations

Purine synthesis promotes maintenance of brain tumor initiating cells in glioma

Wang, X., Yang, K., Xie, Q., Wu, Q., Mack, S. C., Shi, Y., Kim, L. J. Y., Prager, B. C., Flavahan, W. A., Liu, X., Singer, M., Hubert, C. G., Miller, T. E., Zhou, W., Huang, Z., Fang, X., Regev, A., Suvà, M. L., Hwang, T. H., Locasale, J. W. & 2 others, Bao, S. & Rich, J. N., May 1 2017, In : Nature Neuroscience. 20, 5, p. 661-673 13 p.

Research output: Contribution to journalArticle

32 Scopus citations

Robust and efficient identification of biomarkers by classifying features on graphs

Hwang, T., Sicotte, H., Tian, Z., Wu, B., Kocher, J. P., Wigle, D. A., Kumar, V. & Kuang, R., Sep 1 2008, In : Bioinformatics. 24, 18, p. 2023-2029 7 p.

Research output: Contribution to journalArticle

26 Scopus citations

SH3BP4 Is a Negative Regulator of Amino Acid-Rag GTPase-mTORC1 Signaling

Kim, Y. M., Stone, M., Hwang, T. H., Kim, Y. G., Dunlevy, J. R., Griffin, T. J. & Kim, D. H., Jun 29 2012, In : Molecular cell. 46, 6, p. 833-846 14 p.

Research output: Contribution to journalArticle

50 Scopus citations

SHEAR: Sample heterogeneity estimation and assembly by reference

Landman, S. R., Hwang, T. H., Silverstein, K. A. T., Li, Y., Dehm, S. M., Steinbach, M. & Kumar, V., Jan 29 2014, In : BMC Genomics. 15, 1, 84.

Research output: Contribution to journalArticle

3 Scopus citations

SMARCA4-inactivating mutations increase sensitivity to Aurora kinase A inhibitor VX-680 in non-small cell lung cancers

Tagal, V., Wei, S., Zhang, W., Brekken, R. A., Posner, B. A., Peyton, M., Girard, L., Hwang, T., Wheeler, D. A., Minna, J. D., White, M. A., Gazdar, A. F. & Roth, M. G., Jan 19 2017, In : Nature Communications. 8, 14098.

Research output: Contribution to journalArticle

27 Scopus citations

Sparse robust matrix tri-factorization with application to cancer genomics

Kim, S. J., Hwang, T. & Giannakis, G. B., Aug 13 2012, 2012 3rd International Workshop on Cognitive Information Processing, CIP 2012. 6232906. (2012 3rd International Workshop on Cognitive Information Processing, CIP 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

TALEN-engineered AR gene rearrangements reveal endocrine uncoupling of androgen receptor in prostate cancer

Nyquist, M. D., Li, Y., Hwang, T. H., Manlove, L. S., Vessella, R. L., Silverstein, K. A. T., Voytas, D. F. & Dehm, S. M., Oct 22 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 43, p. 17492-17497 6 p.

Research output: Contribution to journalArticle

89 Scopus citations

Targeting renal cell carcinoma with a HIF-2 antagonist

Chen, W., Hill, H., Christie, A., Kim, M. S., Holloman, E., Pavia-Jimenez, A., Homayoun, F., Ma, Y., Patel, N., Yell, P., Hao, G., Yousuf, Q., Joyce, A., Pedrosa, I., Geiger, H., Zhang, H., Chang, J., Gardner, K. H., Bruick, R. K., Reeves, C. & 14 others, Hwang, T. H., Courtney, K., Frenkel, E., Sun, X., Zojwalla, N., Wong, T., Rizzi, J. P., Wallace, E. M., Josey, J. A., Xie, Y., Xie, X. J., Kapur, P., McKay, R. M. & Brugarolas, J., 2016, In : Nature. 539, 7627, p. 112-117 6 p.

Research output: Contribution to journalArticle

205 Scopus citations

Transfer learning across ontologies for phenome-genome association prediction

Petegrosso, R., Park, S., Hwang, T. H. & Kuang, R., Feb 15 2017, In : Bioinformatics. 33, 4, p. 529-536 8 p.

Research output: Contribution to journalArticle

6 Scopus citations

Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer

Henzler, C., Li, Y., Yang, R., McBride, T., Ho, Y., Sprenger, C., Liu, G., Coleman, I., Lakely, B., Li, R., Ma, S., Landman, S. R., Kumar, V., Hwang, T. H., Raj, G. V., Higano, C. S., Morrissey, C., Nelson, P. S., Plymate, S. R. & Dehm, S. M., Nov 29 2016, In : Nature Communications. 7, 13668.

Research output: Contribution to journalArticle

65 Scopus citations