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1

Model-Based and Model-Free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering

Tang, Ming, Gao, Chao, Goutman, Stephen A., Kalinin, Alexandr, Mukherjee, Bhramar, Guan, Yuanfang, Dinov, Ivo D.

Journal:

Neuroinformatics

Year:

2018

Language:

english

File:

PDF, 1.58 MB

english, 2018

2

Predicting human olfactory perception from chemical features of odor molecules

Keller, Andreas, Gerkin, Richard C., Guan, Yuanfang, Dhurandhar, Amit, Turu, Gabor, Szalai, Bence, Mainland, Joel D., Ihara, Yusuke, Yu, Chung Wen, Wolfinger, Russ, Vens, Celine, Schietgat, Leander, D

Journal:

Year:

2017

Language:

english

File:

PDF, 2.93 MB

english, 2017

3

Challenge-Enabled Machine Learning to Drug-Response Prediction

Wang, Ziyan, Li, Hongyang, Carpenter, Christopher, Guan, Yuanfang

Journal:

The AAPS Journal

Year:

2020

File:

PDF, 539 KB

2020

4

Dual transcriptional control of claudin-11 via an overlapping GATA/NF-Y motif: Positive regulation through the interaction of GATA, NF-YA, and CREB and negative regulation through the interaction of Smad, HDAC1, and mSin3A

Wing-Yee Lui, Elissa W.P. Wong, Yuanfang Guan, Will M. Lee

Journal:

Journal of Cellular Physiology

Year:

2007

Language:

english

File:

PDF, 437 KB

english, 2007

5

Nucleosome-coupled expression differences in closely-related species

Yuanfang Guan, Victoria Yao, Kyle Tsui, Marinella Gebbia, Maitreya J Dunham, Corey Nislow, Olga G Troyanskaya

Journal:

Year:

2011

Language:

english

File:

PDF, 782 KB

english, 2011

6

Testing the mutagenicity of five pesticides with micronucleus technique ofTradescantia paludosa

Xu Laixiang, Lu Yuanfang, Guan Weijun, Kong Fanhua, Tang Meiyi

Journal:

Journal of Forestry Research

Year:

1994

Language:

english

File:

PDF, 202 KB

english, 1994

7

Expression of pigment epithelium-derived factor in bladder tumour is correlated with interleukin-8 yet not with interleukin-1α

Chenchen Feng, Ming Guan, Qiang Ding, Yuanfang Zhang, Haowen Jiang, Hui Wen, Paohsun Wang, Zhong Wu

Journal:

Journal of Huazhong University of Science and Technology -- Medical Sciences --

Year:

2011

Language:

english

File:

PDF, 453 KB

english, 2011

8

Using Tree Analysis Pattern and SELDI-TOF-MS to Discriminate Transitional Cell Carcinoma of the Bladder Cancer from Noncancer Patients

Weiwei Liu, Ming Guan, Denglong Wu, Yuanfang Zhang, Zhong Wu, Ming Xu, Yuan Lu

Journal:

European Urology

Year:

2005

Language:

english

File:

PDF, 394 KB

english, 2005

9

Comparative gene expression between two yeast species

Guan, Yuanfang, Dunham, Maitreya J, Troyanskaya, Olga G, Caudy, Amy A

Journal:

Year:

2013

Language:

english

File:

PDF, 797 KB

english, 2013

10

Predicting gene function in a hierarchical context with an ensemble of classifiers

Yuanfang Guan, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy…

Journal:

Year:

2008

Language:

english

File:

PDF, 2.76 MB

english, 2008

11

A new class of protein cancer biomarker candidates: Differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines

Omenn, Gilbert S., Guan, Yuanfang, Menon, Rajasree

Journal:

Journal of Proteomics

Year:

2014

Language:

english

File:

PDF, 1.13 MB

english, 2014

12

The emerging era of genomic data integration for analyzing splice isoform function

Li, Hong-Dong, Menon, Rajasree, Omenn, Gilbert S., Guan, Yuanfang

Journal:

Trends in Genetics

Year:

2014

Language:

english

File:

PDF, 1.24 MB

english, 2014

13

Identification of Stage-Specific Genes Associated With Lupus Nephritis and Response to Remission Induction in (NZB × NZW)F1 and NZM2410 Mice

Bethunaickan, Ramalingam, Berthier, Celine C., Zhang, Weijia, Eksi, Ridvan, Li, Hong-Dong, Guan, Yuanfang, Kretzler, Matthias, Davidson, Anne

Journal:

Arthritis & Rheumatology

Year:

2014

Language:

english

File:

PDF, 5.16 MB

english, 2014

14

Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence

Li, Hong-Dong, Menon, Rajasree, Omenn, Gilbert S., Guan, Yuanfang

Journal:

Year:

2014

Language:

english

File:

PDF, 450 KB

english, 2014

15

Incorporation of N0 Stage with Insufficient Numbers of Lymph Nodes into N1 Stage in the Seventh Edition of the TNM Classification Improves Prediction of Prognosis in Gastric Cancer: Results of a Single-Institution Study of 1258 Chinese Patients

Li, Bofei, Li, Yuanfang, Wang, Wei, Qiu, Haibo, Seeruttun, Sharvesh Raj, Fang, Cheng, Chen, Yongming, Liang, Yao, Li, Wei, Chen, Yingbo, Sun, Xiaowei, Guan, Yuanxiang, Zhan, Youqing, Zhou, Zhiwei

Journal:

Annals of Surgical Oncology

Year:

2016

Language:

english

File:

PDF, 614 KB

english, 2016

16

Regulatory network inferred using expression data of small sample size: application and validation in erythroid system

Zhu, Fan, Shi, Lihong, Engel, James Douglas, Guan, Yuanfang

Journal:

Year:

2015

Language:

english

File:

PDF, 723 KB

english, 2015

17

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations

Guan, Yuanfang, Ackert-Bicknell, Cheryl L., Kell, Braden, Troyanskaya, Olga G., Hibbs, Matthew A., Price, Nathan D.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.03 MB

english, 2010

18

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

Park, Christopher Y., Wong, Aaron K., Greene, Casey S., Rowland, Jessica, Guan, Yuanfang, Bongo, Lars A., Burdine, Rebecca D., Troyanskaya, Olga G., Tucker-Kellogg, Greg

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.94 MB

english, 2013

19

Systematic Planning of Genome-Scale Experiments in Poorly Studied Species

Guan, Yuanfang, Dunham, Maitreya, Caudy, Amy, Troyanskaya, Olga, Searls, David B.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.63 MB

english, 2010

20

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data

Eksi, Ridvan, Li, Hong-Dong, Menon, Rajasree, Wen, Yuchen, Omenn, Gilbert S., Kretzler, Matthias, Guan, Yuanfang, Iakoucheva, Lilia M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.69 MB

english, 2013

21

A Genomewide Functional Network for the Laboratory Mouse

Guan, Yuanfang, Myers, Chad L., Lu, Rong, Lemischka, Ihor R., Bult, Carol J., Troyanskaya, Olga G., Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 1.42 MB

english, 2008

22

Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes

Guan, Yuanfang, Gorenshteyn, Dmitriy, Burmeister, Margit, Wong, Aaron K., Schimenti, John C., Handel, Mary Ann, Bult, Carol J., Hibbs, Matthew A., Troyanskaya, Olga G., Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012

23

Biased, Non-equivalent Gene-Proximal and -Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells

Shi, Lihong, Sierant, M. C., Gurdziel, Katherine, Zhu, Fan, Cui, Shuaiying, Kolodziej, Katarzyna E., Strouboulis, John, Guan, Yuanfang, Tanabe, Osamu, Lim, Kim-Chew, Engel, James Douglas, Snyder, Mich

Journal:

Year:

2014

Language:

english

File:

PDF, 1.66 MB

english, 2014

24

Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER–/PR– Breast Cancers, a Chromosome 17 C-HPP Study

Menon, Rajasree, Panwar, Bharat, Eksi, Ridvan, Kleer, Celina, Guan, Yuanfang, Omenn, Gilbert S.

Journal:

Journal of Proteome Research

Year:

2015

Language:

english

File:

PDF, 1.20 MB

english, 2015

25

MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome

Panwar, Bharat, Menon, Rajasree, Eksi, Ridvan, Omenn, Gilbert S., Guan, Yuanfang

Journal:

Journal of Proteome Research

Year:

2015

Language:

english

File:

PDF, 864 KB

english, 2015

26

Functional Networks of Highest-Connected Splice Isoforms, from the Chromosome 17 Human Proteome Project

Li, Hongdong, Menon, Rajasree, Govindarajoo, Brandon, Panwar, Bharat, Zhang, Yang, Omenn, Gilbert S, Guan, Yuanfang

Journal:

Journal of Proteome Research

Year:

2015

Language:

english

File:

PDF, 1.46 MB

english, 2015

27

Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes

Guan, Yuanfang, Martini, Sebastian, Mariani, Laura H.

Journal:

Seminars in Nephrology

Year:

2015

Language:

english

File:

PDF, 1.58 MB

english, 2015

28

Algorithms for modeling global and context-specific functional relationship networks

Zhu, Fan, Panwar, Bharat, Guan, Yuanfang

Journal:

Briefings in Bioinformatics

Year:

2015

Language:

english

File:

PDF, 788 KB

english, 2015

29

Prognostic Significance of Carcinoembryonic Antigen Staining in Cancer Tissues of Gastric Cancer Patients

Wang, Wei, Seeruttun, Sharvesh Raj, Fang, Cheng, Chen, Jiewei, Li, Yong, Liu, Zhimin, Zhan, Youqing, Li, Wei, Chen, Yingbo, Sun, Xiaowei, Li, Yuanfang, Xu, Dazhi, Guan, Yuanxiang, Zhou, Zhiwei

Journal:

Annals of Surgical Oncology

Year:

2016

Language:

english

File:

PDF, 3.01 MB

english, 2016

30

A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling

Li, Hong-Dong, Omenn, Gilbert S., Guan, Yuanfang

Journal:

Briefings in Bioinformatics

Year:

2016

Language:

english

File:

PDF, 557 KB

english, 2016

31

Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning

Panwar, Bharat, Menon, Rajasree, Eksi, Ridvan, Li, Hongdong, Omenn, Gilbert S, Guan, Yuanfang

Journal:

Journal of Proteome Research

Year:

2016

Language:

english

File:

PDF, 1019 KB

english, 2016

32

Rescue of Metabolic Alterations in AR113Q Skeletal Muscle by Peripheral Androgen Receptor Gene Silencing

Giorgetti, Elisa, Yu, Zhigang, Chua, Jason P., Shimamura, Ryosuke, Zhao, Lili, Zhu, Fan, Venneti, Sriram, Pennuto, Maria, Guan, Yuanfang, Hung, Gene, Lieberman, Andrew P.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.71 MB

english, 2016

33

COMPASS: A computational model to predict changes in MMSE scores 24-months after initial assessment of Alzheimer’s disease

Zhu, Fan, Panwar, Bharat, Dodge, Hiroko H., Li, Hongdong, Hampstead, Benjamin M., Albin, Roger L., Paulson, Henry L., Guan, Yuanfang

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

34

A Network of Splice Isoforms for the Mouse

Li, Hong-Dong, Menon, Rajasree, Eksi, Ridvan, Guerler, Aysam, Zhang, Yang, Omenn, Gilbert S., Guan, Yuanfang

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.32 MB

english, 2016

35

GATA3 abundance is a critical determinant of T cell receptor beta allelic exclusion

Ku, Chia-Jui, Sekiguchi, JoAnn M., Panwar, Bharat, Guan, Yuanfang, Takahashi, Satoru, Yoh, Keigyou, Maillard, Ivan, Hosoya, Tomonori, Engel, James Douglas

Journal:

Molecular and Cellular Biology

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

36

miRmine: A Database of Human miRNA Expression Profiles

Panwar, Bharat, Omenn, Gilbert S., Guan, Yuanfang

Journal:

Year:

2017

Language:

english

File:

PDF, 1.09 MB

english, 2017

37

Comparison of spinocerebellar ataxia type 3 mouse models identifies early gain-of-function, cell-autonomous transcriptional changes in oligodendrocytes

Ramani, Biswarathan, Panwar, Bharat, Moore, Lauren R., Wang, Bo, Huang, Rogerio, Guan, Yuanfang, Paulson, Henry L.

Journal:

Human Molecular Genetics

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

38

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gönen, Mehmet, Weir, Barbara A., Cowley, Glenn S., Vazquez, Francisca, Guan, Yuanfang, Jaiswal, Alok, Karasuyama, Masayuki, Uzunangelov, Vladislav, Wang, Tao, Tsherniak, Aviad, Howell, Sara, Marbach,

Journal:

Year:

2017

Language:

english

File:

PDF, 2.22 MB

english, 2017

39

A comprehensive analysis comparing the eighth AJCC gastric cancer pathological classification to the seventh, sixth, and fifth editions

Seeruttun, Sharvesh Raj, Yuan, Shuqiang, Qiu, Haibo, Huang, Yun, Li, Yuanfang, Liang, Yao, Guan, Yuanxiang, Zhan, Youqing, Li, Wei, Chen, Yingbo, Sun, Xiaowei, Xu, Dazhi, Zhou, Zhiwei

Journal:

Cancer Medicine

Year:

2017

Language:

english

File:

PDF, 560 KB

english, 2017

40

Accurate Prediction of Personalized Olfactory Perception from Large-Scale Chemoinformatic Features

Li, Hongyang, Panwar, Bharat, Omenn, Gilbert S, Guan, Yuanfang

Journal:

Year:

2017

Language:

english

File:

PDF, 1.49 MB

english, 2017

41

Brain-specific functional relationship networks inform autism spectrum disorder gene prediction

Duda, Marlena, Zhang, Hongjiu, Li, Hong-Dong, Wall, Dennis P., Burmeister, Margit, Guan, Yuanfang

Journal:

Translational Psychiatry

Year:

2018

Language:

english

File:

PDF, 1018 KB

english, 2018

42

DNAp: A Pipeline for DNA-seq Data Analysis

Causey, Jason L., Ashby, Cody, Walker, Karl, Wang, Zhiping Paul, Yang, Mary, Guan, Yuanfang, Moore, Jason H., Huang, Xiuzhen

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 1.05 MB

english, 2018

43

YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU

Quang, Daniel, Guan, Yuanfang, Parker, Stephen C J, Hancock, John

Journal:

Year:

2018

Language:

english

File:

PDF, 99 KB

english, 2018

44

Prioritizing Predictive Biomarkers for Gene Essentiality in Cancer Cells with mRNA Expression Data and DNA Copy Number Profile

Guan, Yuanfang, Li, Tingyang, Zhang, Hongjiu, Zhu, Fan, Omenn, Gilbert S, Valencia, Alfonso

Journal:

Year:

2018

Language:

english

File:

PDF, 4.40 MB

english, 2018

45

A similarity-based approach to leverage multi-cohort medical data on the diagnosis and prognosis of Alzheimer's disease

Zhang, Hongjiu, Zhu, Fan, Dodge, Hiroko H, Higgins, Gerald A, Omenn, Gilbert S, Guan, Yuanfang

Journal:

Year:

2018

Language:

english

File:

PDF, 1.26 MB

english, 2018

46

Network Propagation Predicts Drug Synergy in Cancers

Li, Hongyang, Li, Tingyang, Quang, Daniel, Guan, Yuanfang

Journal:

Cancer Research

Year:

2018

Language:

english

File:

PDF, 13.77 MB

english, 2018

47

High-Throughput Single-Cell Sequencing of both TCR-β Alleles

Hosoya, Tomonori, Li, Hongyang, Ku, Chia-Jui, Wu, Qingqing, Guan, Yuanfang, Engel, James Douglas

Journal:

The Journal of Immunology

Year:

2018

Language:

english

File:

PDF, 1.74 MB

english, 2018

48

Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge

Siddiqui, Omer, Zhang, Hongjiu, Guan, Yuanfang, Omenn, Gilbert S.

Journal:

Journal of Proteome Research

Year:

2018

Language:

english

File:

PDF, 3.15 MB

english, 2018

49

TAIJI: Approaching Experimental Replicates-Level Accuracy for Drug Synergy Prediction

Li, Hongyang, Hu, Shuai, Neamati, Nouri, Guan, Yuanfang, Wren, Jonathan

Journal:

Year:

2018

Language:

english

File:

PDF, 278 KB

english, 2018

50

Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression

Menon, Shreya, Lu, Chunxia, Menon, Rajasree, Schwartz, Jessica, Guan, Yuanfang

Journal:

Year:

2016

Language:

english

File:

PDF, 1.47 MB

english, 2016

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