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  • Yidong Chen
2020

Age-associated genes in human mammary gland drive human breast cancer progression

Gu, X., Wang, B., Zhu, H., Zhou, Y., Horning, A. M., Huang, T. H. M., Chen, Y., Houghton, P., Lai, Z., Michalek, J. E. & Sun, L. Z., Jun 15 2020, In : Breast Cancer Research. 22, 1, 64.

Research output: Contribution to journalArticle

Open Access

Convolutional neural network models for cancer type prediction based on gene expression

Mostavi, M., Chiu, Y. C., Huang, Y. & Chen, Y., Apr 3 2020, In : BMC Medical Genomics. 13, 44.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Genetic markers for treatment-related pancreatitis in a cohort of Hispanic children with acute lymphoblastic leukemia

Grimes, A. C., Chen, Y., Bansal, H., Aguilar, C., Perez Prado, L., Quezada, G., Estrada, J. & Tomlinson, G. E., 2020, (Accepted/In press) In : Supportive Care in Cancer.

Research output: Contribution to journalArticle

Inhibitory Interplay of SULT2B1b Sulfotransferase with AKR1C3 Aldo-keto Reductase in Prostate Cancer

Park, S., Song, C. S., Lin, C. L., Jiang, S., Osmulski, P. A., Wang, C. M., Marck, B. T., Matsumoto, A. M., Morrissey, C., Gaczynska, M. E., Chen, Y., Mostaghel, E. A. & Chatterjee, B., Feb 1 2020, In : Endocrinology (United States). 161, 2, bqz042.

Research output: Contribution to journalArticle

Knock-out of Hopx disrupts stemness and quiescence of hematopoietic stem cells in mice

Lin, C. C., Yao, C. Y., Hsu, Y. C., Hou, H. A., Yuan, C. T., Li, Y. H., Kao, C. J., Chuang, P. H., Chiu, Y. C., Chen, Y., Chou, W. C. & Tien, H. F., Jul 9 2020, In : Oncogene. 39, 28, p. 5112-5123 12 p.

Research output: Contribution to journalArticle

Open Access
2019

Activation of the intrinsic fibroinflammatory program in adult pancreatic acinar cells triggered by Hippo signaling disruption

Liu, J., Gao, M., Nipper, M., Deng, J., Sharkey, F. E., Johnson, R. L., Crawford, H. C., Chen, Y. & Wang, P., 2019, In : PLoS biology. 17, 9, e3000418.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Adaptation of an R5 simian-human immunodeficiency virus encoding an HIV clade a envelope with or without ablation of adaptive host immunity: Differential selection of viral mutants

Zhou, M., Humbert, M., Mukhtar, M. M., Scinto, H. B., Vyas, H. K., Lakhashe, S. K., Byrareddy, S. N., Maurer, G., Thorat, S., Owuor, J., Lai, Z., Chen, Y., Griffiths, A., Chenine, A. L., Gumber, S., Villinger, F., Montefiori, D. & Ruprecht, R. M., May 1 2019, In : Journal of Virology. 93, 9, e02267-18.

Research output: Contribution to journalArticle

An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data

Wang, L. J., Zhang, C. W., Su, S. C., Chen, H. I. H., Chiu, Y. C., Lai, Z., Bouamar, H., Ramirez, A. G., Cigarroa, F. G., Sun, L. Z. & Chen, Y., Dec 30 2019, In : BMC genomics. 20, 1007.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

CeL-ID: Cell line identification using RNA-seq data

Mohammad, T. A., Tsai, Y. S., Ameer, S., Chen, H. I. H., Chiu, Y. C. & Chen, Y., Feb 4 2019, In : BMC genomics. 20, 81.

Research output: Contribution to journalArticle

Correction: Predicting drug response of tumors from integrated genomic profiles by deep neural networks (BMC Medical Genomics (2019) 12:1 (18) DOI: 10.1186/s12920-018-0460-9)

Chiu, Y. C., Chen, H. I. H., Zhang, T., Zhang, S., Gorthi, A., Wang, L. J., Huang, Y. & Chen, Y., Aug 12 2019, In : BMC Medical Genomics. 12, 1, 119.

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

Rokita, J. L., Rathi, K. S., Cardenas, M. F., Upton, K. A., Jayaseelan, J., Cross, K. L., Pfeil, J., Egolf, L. E., Way, G. P., Farrel, A., Kendsersky, N. M., Patel, K., Gaonkar, K. S., Modi, A., Berko, E. R., Lopez, G., Vaksman, Z., Mayoh, C., Nance, J., McCoy, K. & 49 others, Haber, M., Evans, K., McCalmont, H., Bendak, K., Böhm, J. W., Marshall, G. M., Tyrrell, V., Kalletla, K., Braun, F. K., Qi, L., Du, Y., Zhang, H., Lindsay, H. B., Zhao, S., Shu, J., Baxter, P., Morton, C., Kurmashev, D., Zheng, S., Chen, Y., Bowen, J., Bryan, A. C., Leraas, K. M., Coppens, S. E., Doddapaneni, H. V., Momin, Z., Zhang, W., Sacks, G. I., Hart, L. S., Krytska, K., Mosse, Y. P., Gatto, G. J., Sanchez, Y., Greene, C. S., Diskin, S. J., Vaske, O. M., Haussler, D., Gastier-Foster, J. M., Kolb, E. A., Gorlick, R., Li, X. N., Reynolds, C. P., Kurmasheva, R. T., Houghton, P. J., Smith, M. A., Lock, R. B., Raman, P., Wheeler, D. A. & Maris, J. M., Nov 5 2019, In : Cell Reports. 29, 6, p. 1675-1689.e9

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods

Zhang, S. Y., Zhang, S. W., Fan, X. N., Meng, J., Chen, Y., Gao, S. J. & Huang, Y., Jan 1 2019, In : PLoS Computational Biology. 15, 1, p. e1006663

Research output: Contribution to journalArticle

13 Scopus citations

Immune sensing of aeroallergen-associated double-stranded RNA triggers an IFN response and modulates type 2 lung inflammation

She, L., Alanazi, H. H., Yan, L., Zou, Y., Sun, Y., Dube, P. H., Brooks, E. G., Barrera, G. D., Lai, Z., Chen, Y., Liu, Y., Zhang, X. & Li, X. D., Nov 1 2019, In : Journal of Immunology. 203, 9, p. 2520-2531 12 p.

Research output: Contribution to journalArticle

2 Scopus citations

Immunogenic Heterogeneity of Renal Cell Carcinoma With Venous Tumor Thrombus

Liss, M. A., Chen, Y., Rodriguez, R., Pruthi, D., Johnson-Pais, T., Wang, H., Mansour, A. & Kaushik, D., Feb 2019, In : Urology. 124, p. 168-173 6 p.

Research output: Contribution to journalArticle

3 Scopus citations

Predicting drug response of tumors from integrated genomic profiles by deep neural networks

Chiu, Y. C., Chen, H. I. H., Zhang, T., Zhang, S., Gorthi, A., Wang, L. J., Huang, Y. & Chen, Y., Jan 31 2019, In : BMC Medical Genomics. 12, 18.

Research output: Contribution to journalArticle

12 Scopus citations
2018

Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme

Chiu, Y. C., Hsiao, T. H., Wang, L. J., Chen, Y. & Chuang, E. Y., Nov 1 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 6, p. 1754-1764 11 p., 7769225.

Research output: Contribution to journalArticle

Cross-talk among writers, readers, and erasers of m6A regulates cancer growth and progression

Panneerdoss, S., Eedunuri, V. K., Yadav, P., Timilsina, S., Rajamanickam, S., Viswanadhapalli, S., Abdelfattah, N., Onyeagucha, B. C., Cui, X., Lai, Z., Mohammad, T. A., Gupta, Y. K., Huang, T. H. M., Huang, Y., Chen, Y. & Rao, M. K., Oct 3 2018, In : Science advances. 4, 10, eaar8263.

Research output: Contribution to journalArticle

39 Scopus citations

Erratum to: EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma (Nature, (2018), 555, 7696, (387-391), 10.1038/nature25748)

Gorthi, A., Romero, J. C., Loranc, E., Cao, L., Lawrence, L. A., Goodale, E., Iniguez, A. B., Bernard, X., Masamsetti, V. P., Roston, S., Lawlor, E. R., Toretsky, J. A., Stegmaier, K., Lessnick, S. L., Chen, Y. & Bishop, A. J. R., Jul 26 2018, In : Nature. 559, 7715, p. E11

Research output: Contribution to journalComment/debate

EWS-FLI1 increases transcription to cause R-Loops and block BRCA1 repair in Ewing sarcoma

Gorthi, A., Romero, J. C., Loranc, E., Cao, L., Lawrence, L. A., Goodale, E., Iniguez, A. B., Bernard, X., Masamsetti, V. P., Roston, S., Lawlor, E. R., Toretsky, J. A., Stegmaier, K., Lessnick, S. L., Chen, Y. & Bishop, A. J., Mar 15 2018, In : Nature. 555, 7696, p. 387-391 5 p.

Research output: Contribution to journalArticle

46 Scopus citations

Germline DNA-repair Gene Mutations and Outcomes in Men with Metastatic Castration-resistant Prostate Cancer Receiving First-line Abiraterone and Enzalutamide

Antonarakis, E. S., Lu, C., Luber, B., Liang, C., Wang, H., Chen, Y., Silberstein, J. L., Piana, D., Lai, Z., Chen, Y., Isaacs, W. B. & Luo, J., Jan 1 2018, (Accepted/In press) In : European Urology.

Research output: Contribution to journalArticle

51 Scopus citations

GSAE: An autoencoder with embedded gene-set nodes for genomics functional characterization

Chen, H. I. H., Chiu, Y. C., Zhang, T., Zhang, S., Huang, Y. & Chen, Y., Dec 21 2018, In : BMC Systems Biology. 12, 142.

Research output: Contribution to journalArticle

9 Scopus citations

MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data

Cui, X., Zhang, L., Meng, J., Rao, M. K., Chen, Y. & Huang, Y., Mar 1 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 2, p. 526-534 9 p.

Research output: Contribution to journalArticle

15 Scopus citations

MiR-584-5p potentiates vincristine and radiation response by inducing spindle defects and DNA damage in medulloblastoma

Abdelfattah, N., Rajamanickam, S., Panneerdoss, S., Timilsina, S., Yadav, P., Onyeagucha, B. C., Garcia, M., Vadlamudi, R., Chen, Y., Brenner, A., Houghton, P. & Rao, M. K., Dec 1 2018, In : Nature communications. 9, 1, 4541.

Research output: Contribution to journalArticle

12 Scopus citations

scdNet: A computational tool for single-cell differential network analysis

Chiu, Y. C., Hsiao, T. H., Wang, L. J., Chen, Y. & Shao, Y. H. J., Dec 21 2018, In : BMC Systems Biology. 12, 124.

Research output: Contribution to journalArticle

4 Scopus citations

Sorafenib improves alkylating therapy by blocking induced inflammation, invasion and angiogenesis in breast cancer cells

Zanotto-Filho, A., Rajamanickam, S., Loranc, E., Masamsetti, V. P., Gorthi, A., Romero, J. C., Tonapi, S., Gonçalves, R. M., Reddick, R. L., Benavides, R., Kuhn, J., Chen, Y. & Bishop, A. J. R., Jul 1 2018, In : Cancer Letters. 425, p. 101-115 15 p.

Research output: Contribution to journalArticle

9 Scopus citations

Topological characterization of human and mouse M5C epitranscriptome revealed by bisulfite sequencing

Wei, Z., Panneerdoss, S., Timilsina, S., Zhu, J., Mohammad, T. A., Lu, Z. L., De Magalhães, J. P., Chen, Y., Rong, R., Huang, Y., Rao, M. K. & Meng, J., Jan 1 2018, In : International Journal of Genomics. 2018, 1351964.

Research output: Contribution to journalArticle

7 Scopus citations

Tp53 deficiency causes a wide tumor spectrum and increases embryonal rhabdomyosarcoma metastasis in zebrafish

Ignatius, M. S., Hayes, M. N., Moore, F. E., Tang, Q., Garcia, S. P., Blackburn, P. R., Baxi, K., Wang, L., Jin, A., Ramakrishnan, A., Reeder, S., Chen, Y., Nielsen, G. P., Chen, E. Y., Hasserjian, R. P., Tirode, F., Ekker, S. C. & Langenau, D. M., Sep 2018, In : eLife. 7, e37202.

Research output: Contribution to journalArticle

11 Scopus citations

Utilizing cancer - Functional gene set - Compound networks to identify putative drugs for breast cancer

Hsiao, T. H., Chiu, Y. C., Chen, Y. H., Hsu, Y. C., Chen, H. I. H., Chuang, E. Y. & Chen, Y., Jan 1 2018, In : Combinatorial Chemistry and High Throughput Screening. 21, 2, p. 74-83 10 p.

Research output: Contribution to journalArticle

1 Scopus citations
2017

A novel role of astrocyte elevated gene-1 (AEG-1) in regulating nonalcoholic steatohepatitis (NASH)

Srivastava, J., Robertson, C. L., Ebeid, K., Dozmorov, M., Rajasekaran, D., Mendoza, R., Siddiq, A., Akiel, M. A., Jariwala, N., Shen, X. N., Windle, J. J., Subler, M. A., Mukhopadhyay, N. D., Giashuddin, S., Ghosh, S., Lai, Z., Chen, Y., Fisher, P. B., Salem, A. K., Sanyal, A. J. & 1 others, Sarkar, D., Aug 2017, In : Hepatology. 66, 2, p. 466-480 15 p.

Research output: Contribution to journalArticle

5 Scopus citations

Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net

Zhang, L., Liu, H., Huang, Y., Wang, X., Chen, Y. & Meng, J., Jan 1 2017, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 14, 1, p. 145-154 10 p.

Research output: Contribution to journalArticle

12 Scopus citations

Computational tools for genome-wide R-loops identification and characterisation

Liu, R., Gorthi, A., Jin, Y., Bishop, A. J. R. & Chen, Y., 2017, In : International Journal of Computational Biology and Drug Design. 10, 2, p. 123-136 14 p.

Research output: Contribution to journalArticle

1 Scopus citations

Cross-talk between miR-471-5p and autophagy component proteins regulates LC3-associated phagocytosis (LAP) of apoptotic germ cells

Panneerdoss, S., Viswanadhapalli, S., Abdelfattah, N., Onyeagucha, B. C., Timilsina, S., Mohammad, T. A., Chen, Y., Drake, M., Vuori, K., Kumar, T. R. & Rao, M. K., Dec 1 2017, In : Nature communications. 8, 1, 598.

Research output: Contribution to journalArticle

16 Scopus citations

Differential correlation analysis of lioblastoma reveals immune ceRNA interactions predictive of patient survival

Chiu, Y. C., Wang, L. J., Lu, T. P., Hsiao, T. H., Chuang, E. Y. & Chen, Y., 2017, In : BMC Bioinformatics. 18, 1, 132.

Research output: Contribution to journalArticle

8 Scopus citations

Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer

Chiu, Y. C., Wang, L. J., Hsiao, T. H., Chuang, E. Y. & Chen, Y., Oct 3 2017, In : BMC genomics. 18, 679.

Research output: Contribution to journalArticle

1 Scopus citations

Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups

Sumazin, P., Chen, Y., Treviño, L. R., Sarabia, S. F., Hampton, O. A., Patel, K., Mistretta, T. A., Zorman, B., Thompson, P., Heczey, A., Comerford, S., Wheeler, D. A., Chintagumpala, M., Meyers, R., Rakheja, D., Finegold, M. J., Tomlinson, G., Parsons, D. W. & López-Terrada, D., Jan 1 2017, In : Hepatology. 65, 1, p. 104-121 18 p.

Research output: Contribution to journalArticle

51 Scopus citations

IGFBP7 deletion promotes hepatocellular carcinoma

Akiel, M., Guo, C., Li, X., Rajasekaran, D., Mendoza, R. G., Robertson, C. L., Jariwala, N., Yuan, F., Subler, M. A., Windle, J., Garcia, D. K., Lai, Z., Chen, H. I. H., Chen, Y., Giashuddin, S., Fisher, P. B., Wang, X. Y. & Sarkar, D., Aug 1 2017, In : Cancer Research. 77, 15, p. 4014-4025 12 p.

Research output: Contribution to journalArticle

9 Scopus citations

Molecular Profiling of Human Induced Pluripotent Stem Cell-Derived Hypothalamic Neurones Provides Developmental Insights into Genetic Loci for Body Weight Regulation

Yao, L., Liu, Y., Qiu, Z., Kumar, S., Curran, J. E., Blangero, J., Chen, Y. & Lehman, D. M., Feb 1 2017, In : Journal of Neuroendocrinology. 29, 2

Research output: Contribution to journalArticle

1 Scopus citations

Novel post-transcriptional and post-translational regulation of pro-apoptotic protein BOK and anti-apoptotic protein Mcl-1 determine the fate of breast cancer cells to survive or die

Onyeagucha, B., Subbarayalu, P., Abdelfattah, N., Rajamanickam, S., Timilsina, S., Guzman, R., Zeballos, C., Eedunuri, V., Bansal, S., Mohammad, T., Chen, Y., Vadlamudi, R. K. & Rao, M. K., Oct 17 2017, In : Oncotarget. 8, 49, p. 85984-85996 13 p.

Research output: Contribution to journalArticle

7 Scopus citations

Sustained NFκB inhibition improves insulin sensitivity but is detrimental to muscle health

Zhang, N., Valentine, J. M., Zhou, Y., Li, M. E., Zhang, Y., Bhattacharya, A., Walsh, M. E., Fischer, K. E., Austad, S. N., Osmulski, P., Gaczynska, M. E., Shoelson, S. E., Van Remmen, H., Chen, H. I., Chen, Y., Liang, H. & Musi, N., Aug 1 2017, In : Aging Cell. 16, 4, p. 847-858 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

Ubiquitin carboxyl-Terminal esterase L1 (UCHL1) is associated with stem-like cancer cell functions in pediatric high-grade glioma

Sanchez-Diaz, P. C., Chang, J. C., Moses, E. S., Dao, T., Chen, Y. & Hung, J. Y., May 1 2017, In : PLoS One. 12, 5, e0176879.

Research output: Contribution to journalArticle

11 Scopus citations

XBSeq2: A fast and accurate quantification of differential expression and differential polyadenylation

Liu, Y., Wu, P., Zhou, J., Johnson-Pais, T. L., Lai, Z., Chowdhury, W. H., Rodriguez, R. & Chen, Y., Oct 3 2017, In : BMC Bioinformatics. 18, 384.

Research output: Contribution to journalArticle

7 Scopus citations
2016

A combined gene expression and functional study reveals the crosstalk between N-Myc and differentiation-inducing microRNAs in neuroblastoma cells

Zhao, Z., Ma, X., Shelton, S. D., Sung, D. C., Li, M., Hernandez, D., Zhang, M., Losiewicz, M. D., Chen, Y., Pertsemlidis, A., Yu, X., Liu, Y. & Du, L., 2016, In : Oncotarget. 7, 48, p. 79372-79387 16 p.

Research output: Contribution to journalArticle

10 Scopus citations

Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential

Dong, Q., Gao, H., Shi, Y., Zhang, F., Gu, X., Wu, A., Wang, D., Chen, Y., Bandyopadhyay, A., Yeh, I. T., Daniel, B. J., Chen, Y., Zou, Y., Rebel, V. L., Walter, C. A., Lu, J., Huang, C. & Sun, L. Z., 2016, In : Aging. 8, 11, p. 2754-2776 23 p.

Research output: Contribution to journalArticle

5 Scopus citations

A hierarchical model for clustering m6A methylation peaks in MeRIP-seq data

Cui, X., Meng, J., Zhang, S., Rao, M. K., Chen, Y. & Huang, Y., Aug 22 2016, In : BMC Genomics. 17, 520.

Research output: Contribution to journalArticle

5 Scopus citations

Alkylating agent-induced NRF2 blocks endoplasmic reticulum stress-mediated apoptosis via control of glutathione pools and protein thiol homeostasis

Zanotto-Filho, A., Pragathi Masamsetti, V., Loranc, E., Tonapi, S. S., Gorthi, A., Bernard, X., Goncalves, R. M., Moreira, J. C. F., Chen, Y. & Bishop, A. J., Dec 1 2016, In : Molecular Cancer Therapeutics. 15, 12, p. 3000-3014 15 p.

Research output: Contribution to journalArticle

20 Scopus citations

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

Cui, X., Meng, J., Zhang, S., Chen, Y. & Huang, Y., Jun 15 2016, In : Bioinformatics. 32, 12, p. i378-i385

Research output: Contribution to journalArticle

29 Scopus citations

A simple gene set-based method accurately predicts the synergy of drug pairs

Hsu, Y. C., Chiu, Y. C., Chen, Y., Hsiao, T. H. & Chuang, E. Y., Aug 26 2016, In : BMC Systems Biology. 10, 66.

Research output: Contribution to journalArticle

7 Scopus citations

Combined gene expression and RNAi screening to identify alkylation damage survival pathways from fly to human

Zanotto-Filho, A., Dashnamoorthy, R., Loranc, E., De Souza, L. H. T., Moreira, J. C. F., Suresh, U., Chen, Y. & Bishop, A. J. R., Apr 2016, In : PloS one. 11, 4, e0153970.

Research output: Contribution to journalArticle

2 Scopus citations