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• 2021

  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., Feb 2021, In: Supportive Care in Cancer. 29, 2, p. 725-731 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Genetic Markers
  • Precursor Cell Lymphoblastic Leukemia-Lymphoma
  • Hispanic Americans
  • Pancreatitis
  • Child
• 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 journal › Article › peer-review

  Open Access

  • Human Mammary Glands
  • Breast Neoplasms
  • Genes
  • Breast
  • Neoplasms

• Campylobacter infection promotes IFNγ-dependent intestinal pathology via ILC3 to ILC1 conversion

  Muraoka, W. T., Korchagina, A. A., Xia, Q., Shein, S. A., Jing, X., Lai, Z., Weldon, K. S., Wang, L. J., Chen, Y., Kummer, L. W., Mohrs, M., Vivier, E., Koroleva, E. P. & Tumanov, A. V., 2020, (Accepted/In press) In: Mucosal Immunology.

  Research output: Contribution to journal › Article › peer-review

  • Campylobacter Infections
  • Lymphocytes
  • Campylobacter jejuni
  • Pathology
  • Enterocolitis
  1 Scopus citations

• Classification of Cancer Types Using Graph Convolutional Neural Networks

  Ramirez, R., Chiu, Y. C., Hererra, A., Mostavi, M., Ramirez, J., Chen, Y., Huang, Y. & Jin, Y. F., Jun 17 2020, In: Frontiers in Physics. 8, 203.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cancer
  • cancer
  • Neural Networks
  • Proteins
  • Neural networks

• 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 journal › Article › peer-review

  Open Access

  • Neural Networks (Computer)
  • Gene Expression
  • Neoplasms
  • Neoplasm Genes
  • Transcriptome
  5 Scopus citations

• Evaluation of eribulin combined with irinotecan for treatment of pediatric cancer xenografts

  Robles, A. J., Kurmasheva, R. T., Bandyopadhyay, A., Phelps, D. A., Erickson, S. W., Lai, Z., Kurmashev, D., Chen, Y., Smith, M. A. & Houghton, P. J., Jun 15 2020, In: Clinical Cancer Research. 26, 12, p. 3012-3023 12 p.

  Research output: Contribution to journal › Article › peer-review

  • eribulin
  • Irinotecan
  • Heterografts
  • Pediatrics
  • Vincristine
  2 Scopus citations

• 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 journal › Article › peer-review

  • Aldo-Keto Reductases
  • Sulfotransferases
  • Androgen Receptors
  • Prostatic Neoplasms
  • Castration

• 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 journal › Article › peer-review

  • Hematopoietic Stem Cells
  • Acute Myeloid Leukemia
  • Bone Marrow
  • Hematopoiesis
  • Leukemia
  2 Scopus citations

• Microbiome within Primary Tumor Tissue from Renal Cell Carcinoma May Be Associated with PD-L1 Expression of the Venous Tumor Thrombus

  Liss, M. A., Chen, Y., Rodriguez, R., Pruthi, D., Johnson-Pais, T., Wang, H., Mansour, A., White, J. R. & Kaushik, D., 2020, In: Advances in Urology. 2020, 9068068.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Microbiota
  • Renal Cell Carcinoma
  • Thrombosis
  • Neoplasms
  • Proof of Concept Study
  2 Scopus citations

• Necroptosis-based CRISPR knockout screen reveals Neuropilin-1 as a critical host factor for early stages of murine cytomegalovirus infection

  Lane, R. K., Guo, H., Fisher, A. D., Diep, J., Lai, Z., Chen, Y., Upton, J. W., Carette, J., Mocarski, E. S. & Kaiser, W. J., Aug 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 33, p. 20109-20116 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Neuropilin-1
  • Muromegalovirus
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Cytomegalovirus Infections
  • Herpesviridae Infections

• Predicting Sites of Epitranscriptome Modifications Using Unsupervised Representation Learning Based on Generative Adversarial Networks

  Salekin, S., Mostavi, M., Chiu, Y. C., Chen, Y., Zhang, J. & Huang, Y., Jun 19 2020, In: Frontiers in Physics. 8, 196.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • learning
  • Learning
  • Pseudouridine
  • embedding
  • RNA Precursors

• Scaffold Architecture and Matrix Strain Modulate Mesenchymal Cell and Microvascular Growth and Development in a Time Dependent Manner

  Chiou, G., Jui, E., Rhea, A. C., Gorthi, A., Miar, S., Acosta, F. M., Perez, C., Suhail, Y., Kshitiz, Chen, Y., Ong, J. L., Bizios, R., Rathbone, C. & Guda, T., Oct 1 2020, In: Cellular and Molecular Bioengineering. 13, 5, p. 507-526 20 p.

  Research output: Contribution to journal › Article › peer-review

  • Scaffolds (biology)
  • Scaffold
  • Cell growth
  • Scaffolds
  • Architecture
• 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 journal › Article › peer-review

  Open Access

  • acinar cells
  • Acinar Cells
  • Chemical activation
  • Tissue
  • Pancreatic Stellate Cells
  4 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 journal › Article › peer-review

  • Human immunodeficiency virus
  • Simian Immunodeficiency Virus
  • Adaptive Immunity
  • immunity
  • HIV

• 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 journal › Article › peer-review

  Open Access

  • Whole Exome Sequencing
  • Hispanic Americans
  • Single Nucleotide Polymorphism
  • Genome
  • Population
  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 journal › Article › peer-review

  • RNA
  • Cell Line
  • Benchmarking
  • Quality Control
  • Linear Models
  1 Scopus citations

• 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 journal › Comment/debate › peer-review

  Open Access

  • Genomics
  • National Center for Advancing Translational Sciences (U.S.)
  • Publications
  • Biological Science Disciplines
  • Pharmaceutical Preparations
  2 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 journal › Article › peer-review

  Open Access

  • Pediatrics
  • Tumors
  • Histology
  • Heterografts
  • Clinical Trials
  16 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., 2019, In: PLoS computational biology. 15, 1, e1006663.

  Research output: Contribution to journal › Article › peer-review

  • N(6)-methyladenosine
  • Deep Learning
  • Global Analysis
  • Deep learning
  • learning
  16 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 journal › Article › peer-review

  • Pyroglyphidae
  • Double-Stranded RNA
  • Pneumonia
  • Allergens
  • Eosinophilia
  4 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 journal › Article › peer-review

  • Renal Cell Carcinoma
  • Thrombosis
  • Ligands
  • Macrophages
  • Neoplasms
  5 Scopus citations

• PD03-01 RNASEQ MICROBIAL ANALYSIS IDENTIFY VARIABILITY BETWEEN RENAL CELL CARCINOMA PRIMARY TUMOR AND INTRAVASCULAR TUMOR EXTENSION

  Liss, M., Kaushik, D., Chen, Y., Johnson-Pais, T., Pruthi, D., Mansour, A., White, J. & Rodriguez, R., Apr 1 2019, In: The Journal of urology. 201, p. e67

  Research output: Contribution to journal › Article › peer-review

  • Renal Cell Carcinoma
  • Thrombosis
  • Neoplasms
  • Microbiota
  • Kidney Neoplasms

• 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 journal › Article › peer-review

  • Pharmaceutical Preparations
  • Neoplasms
  • Pharmacogenetics
  • Deep Learning
  • Neural Networks (Computer)
  26 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 journal › Article › peer-review

  • Regulatory Networks
  • Modulator
  • Genomics
  • Gene Regulatory Networks
  • Gene Regulatory Network

• 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 journal › Article › peer-review

  • Methyltransferases
  • Growth
  • Genes
  • N(6)-methyladenosine
  • Neoplasms
  64 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 journal › Comment/debate › peer-review

  • sarcoma

• 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. R., Mar 15 2018, In: Nature. 555, 7696, p. 387-391 5 p.

  Research output: Contribution to journal › Article › peer-review

  • EWS-FLI fusion protein
  • Ewing's Sarcoma
  • Homologous Recombination
  • RNA-Binding Protein EWS
  • Genetic Translocation
  62 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., Aug 2018, In: European Urology. 74, 2, p. 218-225 8 p.

  Research output: Contribution to journal › Article › peer-review

  • abiraterone
  • MDV 3100
  • Castration
  • DNA Repair
  • Prostatic Neoplasms
  70 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 journal › Article › peer-review

  • Functional Genomics
  • Genomics
  • Gene
  • Genes
  • Vertex of a graph
  11 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 journal › Article › peer-review

  • Methylation
  • RNA
  • Sequencing
  • RNA Sequence Analysis
  • Immunoprecipitation
  19 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 journal › Article › peer-review

  • Stem cells
  • spindles
  • Medulloblastoma
  • Vincristine
  • Tumors
  20 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 journal › Article › peer-review

  • Network Analysis
  • Sequencing
  • RNA Sequence Analysis
  • Electric network analysis
  • RNA
  7 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 journal › Article › peer-review

  • Sorafenib
  • Alkylation
  • Breast Neoplasms
  • Inflammation
  • Neoplasm Metastasis
  14 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., 2018, In: International Journal of Genomics. 2018, 1351964.

  Research output: Contribution to journal › Article › peer-review

  • hydrogen sulfite
  • Methylation
  • DNA Methylation
  • Transcriptome
  • RNA
  8 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 journal › Article › peer-review

  • Embryonal Rhabdomyosarcoma
  • Tumors
  • Zebrafish
  • Neoplasm Metastasis
  • Neoplasms
  18 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., 2018, In: Combinatorial Chemistry and High Throughput Screening. 21, 2, p. 74-83 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Neoplasm Genes
  • Genes
  • Breast Neoplasms
  • Oncology
  • Pharmaceutical Preparations
  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 journal › Article › peer-review

  • Non-alcoholic Fatty Liver Disease
  • Astrocytes
  • Genes
  • High Fat Diet
  • Hepatocytes
  7 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 journal › Article › peer-review

  • Elastic Net
  • Progression
  • Cancer
  • Gene
  • Genes
  17 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 journal › Article › peer-review

  • DNA
  • Genes
  • RNA
  • Genome
  • Gene expression
  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 journal › Article › peer-review

  • Germ Cells
  • Sertoli Cells
  • Phagocytosis
  • Autophagy
  • Cells
  19 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 journal › Article › peer-review

  • Correlation Analysis
  • RNA
  • MicroRNA
  • Interaction
  • Survival
  11 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 journal › Article › peer-review

  • Gene Regulatory Networks
  • Genome
  • Breast Neoplasms
  • Genes
  • Estrogen Receptors
  2 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 journal › Article › peer-review

  • Hepatoblastoma
  • Biomarkers
  • AT-Hook Motifs
  • Hepatocyte Nuclear Factor 1
  • oncofetal antigens
  65 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 journal › Article › peer-review

  • Hepatocellular Carcinoma
  • Neoplasms
  • Cross-Priming
  • Insulin-Like Growth Factor Binding Proteins
  • Antigen Presentation
  16 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 journal › Article › peer-review

  • Genetic Loci
  • Induced Pluripotent Stem Cells
  • Body Weight
  • Neurons
  • Transcriptome
  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 journal › Article › peer-review

  • Myeloid Leukemia
  • Apoptosis Regulatory Proteins
  • Myeloid Cells
  • Breast Neoplasms
  • Apoptosis
  13 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., Shoelson, S. E., Van Remmen, H., Chen, H. I., Chen, Y., Liang, H. & Musi, N., Aug 2017, In: Aging cell. 16, 4, p. 847-858 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Sarcopenia
  • Insulin Resistance
  • Muscles
  • Health
  • Myostatin
  9 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 2017, In: PloS one. 12, 5, e0176879.

  Research output: Contribution to journal › Article › peer-review

  • Pediatrics
  • glioma
  • pediatrics
  • Esterases
  • ubiquitin
  16 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 journal › Article › peer-review

  • Polyadenylation
  • Differential Expression
  • RNA
  • Sequencing
  • RNA Sequence Analysis
  8 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 journal › Article › peer-review

  • Neuroblastoma
  • MicroRNAs
  • Gene Expression
  • Cell Differentiation
  • Carcinogenesis
  10 Scopus citations