Yufei Huang, Ph.D. - Publications

Affiliations: 
2001 Stony Brook University, Stony Brook, NY, United States 
Area:
Signal analysis, modeling, and processing; Monte Carlo methods; wireless communications and sensor networks

47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Mostavi M, Chiu YC, Chen Y, Huang Y. CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training. Bmc Bioinformatics. 22: 244. PMID 33980137 DOI: 10.1186/s12859-021-04157-w  0.56
2021 Zhang TH, Flores M, Huang Y. ES-ARCNN: Predicting enhancer strength by using data augmentation and residual convolutional neural network. Analytical Biochemistry. 114120. PMID 33535061 DOI: 10.1016/j.ab.2021.114120  0.4
2021 Ramirez R, Chiu YC, Zhang S, Ramirez J, Chen Y, Huang Y, Jin YF. Prediction and Interpretation of Cancer Survival Using Graph Convolution Neural Networks. Methods (San Diego, Calif.). PMID 33484826 DOI: 10.1016/j.ymeth.2021.01.004  0.56
2020 Ramirez R, Chiu YC, Hererra A, Mostavi M, Ramirez J, Chen Y, Huang Y, Jin YF. Classification of Cancer Types Using Graph Convolutional Neural Networks. Frontiers in Physics. 8. PMID 33437754 DOI: 10.3389/Fphy.2020.00203  0.56
2020 Ko LW, D SVS, Huang Y, Lu YC, Shaw S, Jung TP. SSVEP-assisted RSVP Brain-Computer Interface paradigm for multi-target classification. Journal of Neural Engineering. PMID 33291083 DOI: 10.1088/1741-2552/abd1c0  0.48
2020 Salekin S, Mostavi M, Chiu YC, Chen Y, Zhang JM, Huang Y. Predicting sites of epitranscriptome modifications using unsupervised representation learning based on generative adversarial networks. Frontiers in Physics. 8. PMID 33274189 DOI: 10.3389/Fphy.2020.00196  0.68
2020 Liu L, Song B, Ma J, Song Y, Zhang SY, Tang Y, Wu X, Wei Z, Chen K, Su J, Rong R, Lu Z, de Magalhães JP, Rigden DJ, Zhang L, ... ... Huang Y, et al. Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. Computational and Structural Biotechnology Journal. 18: 1587-1604. PMID 32670500 DOI: 10.1016/J.Csbj.2020.06.010  0.56
2020 Mostavi M, Chiu YC, Huang Y, Chen Y. Convolutional neural network models for cancer type prediction based on gene expression. Bmc Medical Genomics. 13: 44. PMID 32241303 DOI: 10.1186/S12920-020-0677-2  0.56
2019 Chiu YC, Chen HH, Gorthi A, Mostavi M, Zheng S, Huang Y, Chen Y. Deep learning of pharmacogenomics resources: moving towards precision oncology. Briefings in Bioinformatics. PMID 31813953 DOI: 10.1093/Bib/Bbz144  0.56
2019 Huang Y, Li X, Jackson T, Chen S, Meng J, Qiu J, Chen H. Interaction Effect of Sex and Body Mass Index on Gray Matter Volume. Frontiers in Human Neuroscience. 13: 360. PMID 31680912 DOI: 10.3389/Fnhum.2019.00360  0.56
2019 Zhang SY, Zhang SW, Fan XN, Zhang T, Meng J, Huang Y. FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes. Bioinformatics (Oxford, England). 35: i90-i98. PMID 31510685 DOI: 10.1093/Bioinformatics/Btz316  0.56
2019 Chiu YC, Chen HH, Zhang T, Zhang S, Gorthi A, Wang LJ, Huang Y, Chen Y. Correction to: Predicting drug response of tumors from integrated genomic profiles by deep neural networks. Bmc Medical Genomics. 12: 119. PMID 31405368 DOI: 10.1186/S12920-019-0569-5  0.56
2019 Tang Y, Chen K, Wu X, Wei Z, Zhang SY, Song B, Zhang SW, Huang Y, Meng J. DRUM: Inference of Disease-Associated mA RNA Methylation Sites From a Multi-Layer Heterogeneous Network. Frontiers in Genetics. 10: 266. PMID 31001320 DOI: 10.3389/Fgene.2019.00266  0.56
2019 Chiu YC, Chen HH, Zhang T, Zhang S, Gorthi A, Wang LJ, Huang Y, Chen Y. Predicting drug response of tumors from integrated genomic profiles by deep neural networks. Bmc Medical Genomics. 12: 18. PMID 30704458 DOI: 10.1186/S12920-018-0460-9  0.56
2019 Zhang SY, Zhang SW, Fan XN, Meng J, Chen Y, Gao SJ, Huang Y. Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. Plos Computational Biology. 15: e1006663. PMID 30601803 DOI: 10.1371/Journal.Pcbi.1006663  0.56
2018 Chen HH, Chiu YC, Zhang T, Zhang S, Huang Y, Chen Y. GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization. Bmc Systems Biology. 12: 142. PMID 30577835 DOI: 10.1186/S12918-018-0642-2  0.56
2018 Panneerdoss S, Eedunuri VK, Yadav P, Timilsina S, Rajamanickam S, Viswanadhapalli S, Abdelfattah N, Onyeagucha BC, Cui X, Lai Z, Mohammad TA, Gupta YK, Huang TH, Huang Y, Chen Y, et al. Cross-talk among writers, readers, and erasers of mA regulates cancer growth and progression. Science Advances. 4: eaar8263. PMID 30306128 DOI: 10.1126/Sciadv.Aar8263  0.56
2018 Wei Z, Panneerdoss S, Timilsina S, Zhu J, Mohammad TA, Lu ZL, de Magalhães JP, Chen Y, Rong R, Huang Y, Rao MK, Meng J. Topological Characterization of Human and Mouse mC Epitranscriptome Revealed by Bisulfite Sequencing. International Journal of Genomics. 2018: 1351964. PMID 30009162 DOI: 10.1155/2018/1351964  0.56
2018 Salekin S, Zhang JM, Huang Y. Base-pair resolution detection of transcription factor binding site by deep deconvolutional network. Bioinformatics (Oxford, England). PMID 29757349 DOI: 10.1093/Bioinformatics/Bty383  0.68
2018 Cui X, Zhang L, Meng J, Rao MK, Chen Y, Huang Y. MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. Ieee/Acm Transactions On Computational Biology and Bioinformatics. 15: 526-534. PMID 29610101 DOI: 10.1109/Tcbb.2015.2403355  0.56
2018 Zhang L, He Y, Wang H, Liu H, Huang Y, Wang X, Meng J. Clustering Count-based RNA Methylation Data Using a Nonparametric Generative Model Current Bioinformatics. 14: 11-23. DOI: 10.2174/1574893613666180601080008  0.56
2017 Liu H, Wang H, Wei Z, Zhang S, Hua G, Zhang SW, Zhang L, Gao SJ, Meng J, Chen X, Huang Y. MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. Nucleic Acids Research. PMID 29126312 DOI: 10.1093/Nar/Gkx1080  0.56
2017 Tan B, Liu H, Zhang S, da Silva SR, Zhang L, Meng J, Cui X, Yuan H, Sorel O, Zhang SW, Huang Y, Gao SJ. Viral and cellular N(6)-methyladenosine and N(6),2'-O-dimethyladenosine epitranscriptomes in the KSHV life cycle. Nature Microbiology. PMID 29109479 DOI: 10.1038/S41564-017-0056-8  0.56
2017 Liu L, Zhang SW, Huang Y, Meng J. QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model. Bmc Bioinformatics. 18: 387. PMID 28859631 DOI: 10.1186/S12859-017-1808-4  0.56
2016 Zhang S, Zhang S, Liu L, Meng J, Huang Y. m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks. Plos Computational Biology. 12: e1005287. PMID 28027310 DOI: 10.1371/Journal.Pcbi.1005287  0.56
2016 Chen HH, Jin Y, Huang Y, Chen Y. Detection of high variability in gene expression from single-cell RNA-seq profiling. Bmc Genomics. 17: 508. PMID 27556924 DOI: 10.1186/S12864-016-2897-6  0.56
2016 Cui X, Meng J, Zhang S, Rao MK, Chen Y, Huang Y. A hierarchical model for clustering m(6)A methylation peaks in MeRIP-seq data. Bmc Genomics. 17: 520. PMID 27556597 DOI: 10.1186/S12864-016-2913-X  0.56
2016 Ma C, Sastry KS, Flore M, Gehani S, Al-Bozom I, Feng Y, Serpedin E, Chouchane L, Chen Y, Huang Y. CrossLink: a novel method for cross-condition classification of cancer subtypes. Bmc Genomics. 17: 549. PMID 27556419 DOI: 10.1186/S12864-016-2903-Z  0.56
2016 Huang K, Liu Y, Huang Y, Li L, Cooper L, Ruan J, Zhao Z. Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. Bmc Genomics. 17: 524. PMID 27556295 DOI: 10.1186/S12864-016-2893-X  0.88
2016 Cui X, Wei Z, Zhang L, Liu H, Sun L, Zhang SW, Huang Y, Meng J. Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features. Biomed Research International. 2016: 8367534. PMID 27239475 DOI: 10.1155/2016/8367534  0.56
2016 Xu X, Li L, Zhou Z, Sun W, Huang Y. Dual-pH Responsive Micelle Platform for Co-delivery of Axitinib and Doxorubicin. International Journal of Pharmaceutics. PMID 27154256 DOI: 10.1016/j.ijpharm.2016.04.060  0.32
2016 Wang X, Wang M, Zhang Y, Miao X, Huang Y, Zhang J, Sun L. Electrochemical biosensor based on enzyme substrate as a linker: Application for aldolase activity with pectin-thionine complex as recognization element and signal amplification probe. Biosensors & Bioelectronics. 83: 91-96. PMID 27107145 DOI: 10.1016/j.bios.2016.04.009  0.88
2016 Liu L, Zhang SW, Gao F, Zhang Y, Huang Y, Chen R, Meng J. DRME: count-based differential RNA methylation analysis at small sample size scenario. Analytical Biochemistry. PMID 26851340 DOI: 10.1016/J.Ab.2016.01.014  0.56
2016 Dai L, Huang Y, Chen Y, Long Ze. Cloning and characterization of filamentous temperature-sensitive protein Z from Xanthomonas oryzae pv. Oryzae Springerplus. 5: 1-7. DOI: 10.1186/s40064-016-1876-3  0.56
2016 Lu W, Xiao P, Gu J, Zhang J, Huang Y, Huang Q, Chen T. Aggregation-induced emission of tetraphenylethylene-modified polyethyleneimine for highly selective CO2 detection Sensors and Actuators, B: Chemical. 228: 551-556. DOI: 10.1016/J.Snb.2016.01.096  0.32
2016 Fan Y, Li X, Wu X, Li L, Li W, Huang Y. Divergent responses of vegetation aboveground net primary productivity to rainfall pulses in the Inner Mongolian Plateau, China Journal of Arid Environments. 129: 1-8. DOI: 10.1016/j.jaridenv.2016.02.002  0.32
2016 Huang Y, Tong C, Xu F, Chen Y, Zhang C, Bao J. Variation in mineral elements in grains of 20 brown rice accessions in two environments Food Chemistry. 192: 873-878. DOI: 10.1016/j.foodchem.2015.07.087  0.56
2016 Zhang Y, Huang Y, Chen H, Huang Z, Yang Y, Xiao P, Zhou Y, Chen Y. Composition and structure control of ultralight graphene foam for high-performance microwave absorption Carbon. 105: 438-447. DOI: 10.1016/J.Carbon.2016.04.070  0.56
2015 Zhang L, Liu H, Huang Y, Wang X, Chen Y, Meng J. Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28055897 DOI: 10.1109/Tcbb.2015.2511758  0.56
2015 Ma X, Zhu Y, Huang Y, Tegeler T, Gao SJ, Zhang J. Quantitative Proteomic Approach for MicroRNA Target Prediction Based on (18)O/(16)O Labeling. Cancer Informatics. 14: 163-173. PMID 27980386 DOI: 10.4137/Cin.S30563  0.88
2015 Zhang L, Liu H, Huang Y, Wang X, Chen Y, Meng J. Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 26841407 DOI: 10.1109/TCBB.2015.2511758  0.56
2015 Chen HI, Liu Y, Zou Y, Lai Z, Sarkar D, Huang Y, Chen Y. Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads. Bmc Genomics. 16: S14. PMID 26099631 DOI: 10.1186/1471-2164-16-S7-S14  0.88
2015 Ruan J, Jin V, Huang Y, Xu H, Edwards JS, Chen Y, Zhao Z. Education, collaboration, and innovation: intelligent biology and medicine in the era of big data. Bmc Genomics. 16: S1. PMID 26099197 DOI: 10.1186/1471-2164-16-S7-S1  0.56
2015 Cui X, Meng J, Rao MK, Chen Y, Huang Y. HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data. Bmc Genomics. 16: S2. PMID 25917296 DOI: 10.1186/1471-2164-16-S4-S2  0.56
2014 Zhang SW, Zhang TH, Zhang JN, Huang Y. Prediction of Signal Peptide Cleavage Sites with Subsite-Coupled and Template Matching Fusion Algorithm. Molecular Informatics. 33: 230-9. PMID 27485691 DOI: 10.1002/Minf.201300077  0.4
2009 Meng J, Gao SJ, Huang Y. Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. Bioinformatics (Oxford, England). 25: 1521-7. PMID 19351618 DOI: 10.1093/Bioinformatics/Btp235  0.56
2008 Meng J, Gao SJ, Huang Y. An Iterative Time Windowed Signature Algorithm for Time Dependent Transcription Module Discovery. Ieee International Workshop On Genomic Signal Processing and Statistics : [Proceedings]. Ieee International Workshop On Genomic Signal Processing and Statistics. 2008: 1-4. PMID 21552463 DOI: 10.1109/GENSIPS.2008.4555659  0.56
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