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1

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || A Practical Guide to The Cancer Genome Atlas (TCGA)

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 2.13 MB

english, 2016

2

Electronic vs Combustible Cigarette Effects on Inflammasome Component Release into Human Lung

Tsai, MuChun, Song, Min-Ae, McAndrew, Christian, Brasky, Theodore M, Freudenheim, Jo L, Mathé, Ewy, McElroy, Joseph, Reisinger, Sarah A, Shields, Peter G, Wewers, Mark D.

Journal:

American Journal of Respiratory and Critical Care Medicine

Year:

2019

Language:

english

File:

PDF, 172 KB

english, 2019

3

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Introducing Machine Learning Concepts with WEKA

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 652 KB

english, 2016

4

The metaRbolomics Toolbox in Bioconductor and beyond

Stanstrup, Jan, Broeckling, Corey, Helmus, Rick, Hoffmann, Nils, Mathé, Ewy, Naake, Thomas, Nicolotti, Luca, Peters, Kristian, Rainer, Johannes, Salek, Reza, Schulze, Tobias, Schymanski, Emma, Stravs,

Journal:

Year:

2019

Language:

english

File:

PDF, 1.81 MB

english, 2019

5

p53 isoforms Δ133p53 and p53β are endogenous regulators of replicative cellular senescence

Fujita, Kaori, Mondal, Abdul M., Horikawa, Izumi, Nguyen, Giang H., Kumamoto, Kensuke, Sohn, Jane J., Bowman, Elise D., Mathe, Ewy A., Schetter, Aaron J., Pine, Sharon R.

Journal:

Nature Cell Biology

Year:

2009

Language:

english

File:

PDF, 1.95 MB

english, 2009

6

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

Kieffer-Kwon, Kyong-Rim, Tang, Zhonghui, Mathe, Ewy, Qian, Jason, Sung, Myong-Hee, Li, Guoliang, Resch, Wolfgang, Baek, Songjoon, Pruett, Nathanael, Grøntved, Lars, Vian, Laura, Nelson, Steevenson, Za

Journal:

Year:

2013

Language:

english

File:

PDF, 2.77 MB

english, 2013

7

[Methods in Molecular Biology] Statistical Genomics Volume 1418 ||

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 13.93 MB

english, 2016

8

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Overview of Sequence Data Formats

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 186 KB

english, 2016

9

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || The Gene Expression Omnibus Database

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 574 KB

english, 2016

10

A Review of Pulmonary Toxicity of Electronic Cigarettes In The Context of Smoking: A Focus On Inflammation

Shields, Peter G., Berman, Micah, Brasky, Theodore M., Freudenheim, Jo L., Mathe, Ewy A, McElroy, Joseph, Song, Min-Ae, Wewers, Mark D.

Journal:

Cancer Epidemiology Biomarkers & Prevention

Year:

2017

Language:

english

File:

PDF, 1.03 MB

english, 2017

11

The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources

Mathé, Ewy, Hays, John, Stover, Daniel, Chen, James

Journal:

Yearbook of medical informatics

Year:

2018

Language:

english

File:

PDF, 838 KB

english, 2018

12

Electronic Cigarettes and the Lung Proteome

Shields, Peter G, Song, Min-Ae, Freudenheim, Jo L, Brasky, Theodore M, Mathe, Ewy, McElroy, Joseph P, Hummon, Amanda B, Wewers, Mark D

Journal:

American Journal of Respiratory and Critical Care Medicine

Year:

2018

Language:

english

File:

PDF, 77 KB

english, 2018

13

Predicting the transactivation activity of p53 missense mutants using a four-body potential score derived from Delaunay tessellations

Ewy Mathe, Magali Olivier, Shunsuke Kato, Chikashi Ishioka, Iosif Vaisman, Pierre Hainaut

Journal:

Year:

2006

Language:

english

File:

PDF, 261 KB

english, 2006

14

Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database

Audrey Petitjean, Ewy Mathe, Shunsuke Kato, Chikashi Ishioka, Sean V. Tavtigian, Pierre Hainaut, Magali Olivier

Journal:

Year:

2007

Language:

english

File:

PDF, 270 KB

english, 2007

15

Inflammation regulates microRNA expression in cooperation with p53 and nitric oxide

Ewy Mathé, Giang H. Nguyen, Naotake Funamizu, Peijun He, Matthew Moake, Carlo M. Croce, S. Perwez Hussain

Journal:

International Journal of Cancer

Year:

2012

Language:

english

File:

PDF, 577 KB

english, 2012

16

DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes

Hakim, Ofir, Resch, Wolfgang, Yamane, Arito, Klein, Isaac, Kieffer-Kwon, Kyong-Rim, Jankovic, Mila, Oliveira, Thiago, Bothmer, Anne, Voss, Ty C., Ansarah-Sobrinho, Camilo, Mathe, Ewy, Liang, Genqing,

Journal:

Year:

2012

Language:

english

File:

PDF, 1.12 MB

english, 2012

17

[IEEE 2008 IEEE International Conference on Bioinformatics and Biomedicine - Philadelphia, PA, USA (2008.11.3-2008.11.5)] 2008 IEEE International Conference on Bioinformatics and Biomedicine - Structure Based Functional Analysis of Bacteriophage f1 Gene V Protein

Masso, Majid, Mathe, Ewy, Parvez, Nida, Hijazi, Kahkeshan, Vaisman, Iosif I.

Year:

2008

Language:

english

File:

PDF, 696 KB

english, 2008

18

microRNA and inflammatory gene expression as prognostic marker for overall survival in esophageal squamous cell carcinoma

Zhao, Yiqiang, Schetter, Aaron J., Yang, Geoffrey B., Nguyen, Giang, Mathé, Ewy A., Li, Peng, Cai, Hong, Yu, Lei, Liu, Fangfang, Hang, Dong, Yang, Haijun, Wang, Xin Wei, Ke, Yang, Harris, Curtis C.

Journal:

International Journal of Cancer

Year:

2013

Language:

english

File:

PDF, 559 KB

english, 2013

19

B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity

Qian, Jason, Wang, Qiao, Dose, Marei, Pruett, Nathanael, Kieffer-Kwon, Kyong-Rim, Resch, Wolfgang, Liang, Genqing, Tang, Zhonghui, Mathé, Ewy, Benner, Christopher, Dubois, Wendy, Nelson, Steevenson, V

Journal:

Year:

2014

Language:

english

File:

PDF, 2.05 MB

english, 2014

20

[Methods in Molecular Biology] Statistical Genomics Volume 1418 ||

Mathé, Ewy, Davis, Sean

Year:

2016

File:

PDF, 13.93 MB

2016

21

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Experimental Design and Power Calculation for RNA-seq Experiments

Mathé, Ewy, Davis, Sean

Year:

2016

File:

PDF, 195 KB

2016

22

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Experimental Design and Power Calculation for RNA-seq Experiments

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 195 KB

english, 2016

23

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Study Design for Sequencing Studies

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 672 KB

english, 2016

24

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 1.33 MB

english, 2016

25

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Integrative Exploratory Analysis of Two or More Genomic Datasets

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 1.91 MB

english, 2016

26

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Variant Calling From Next Generation Sequence Data

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 266 KB

english, 2016

27

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Genomic Annotation Resources in R/Bioconductor

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 340 KB

english, 2016

28

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 785 KB

english, 2016

29

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Visualizing Genomic Data Using Gviz and Bioconductor

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 1.20 MB

english, 2016

30

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Practical Analysis of Genome Contact Interaction Experiments

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 362 KB

english, 2016

31

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 2.02 MB

english, 2016

32

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 420 KB

english, 2016

33

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Operating on Genomic Ranges Using BEDOPS

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 283 KB

english, 2016

34

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Meta-Analysis in Gene Expression Studies

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 311 KB

english, 2016

35

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 412 KB

english, 2016

36

An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers

Robles, Ana I., Arai, Eri, Mathé, Ewy A., Okayama, Hirokazu, Schetter, Aaron J., Brown, Derek, Petersen, David, Bowman, Elise D., Noro, Rintaro, Welsh, Judith A., Edelman, Daniel C., Stevenson, Holly

Journal:

Journal of Thoracic Oncology

Year:

2015

Language:

english

File:

PDF, 3.91 MB

english, 2015

37

[Methods in Molecular Biology] Statistical Genomics Volume 1418 || Working with Oligonucleotide Arrays

Mathé, Ewy, Davis, Sean

Year:

2016

Language:

english

File:

PDF, 387 KB

english, 2016

38

ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data

Baskin, Elizabeth, Farouni, Rick, Mathé, Ewy A.

Journal:

Year:

2016

Language:

english

File:

PDF, 128 KB

english, 2016

39

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation

Kieffer-Kwon, Kyong-Rim, Nimura, Keisuke, Rao, Suhas S.P., Xu, Jianliang, Jung, Seolkyoung, Pekowska, Aleksandra, Dose, Marei, Stevens, Evan, Mathe, Ewy, Dong, Peng, Huang, Su-Chen, Ricci, Maria Aurel

Journal:

Year:

2017

Language:

english

File:

PDF, 4.33 MB

english, 2017

40

ALTRE: workflow for defining ALTered regulatory elements using chromatin accessibility data

Baskin, Elizabeth, Farouni, Rick, Mathé, Ewy A.

Journal:

Year:

2017

File:

PDF, 41 KB

2017

41

IntLIM: integration using linear models of metabolomics and gene expression data

Siddiqui, Jalal K., Baskin, Elizabeth, Liu, Mingrui, Cantemir-Stone, Carmen Z., Zhang, Bofei, Bonneville, Russell, McElroy, Joseph P., Coombes, Kevin R., Mathé, Ewy A.

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

42

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

Zhang, Bofei, Hu, Senyang, Baskin, Elizabeth, Patt, Andrew, Siddiqui, Jalal, Mathé, Ewy

Journal:

Year:

2018

Language:

english

File:

PDF, 2.75 MB

english, 2018

43

Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS)

Playdon, Mary C., Joshi, Amit D., Tabung, Fred K., Cheng, Susan, Henglin, Mir, Kim, Andy, Lin, Tengda, van Roekel, Eline H., Huang, Jiaqi, Krumsiek, Jan, Wang, Ying, Mathé, Ewy, Temprosa, Marinella, M

Journal:

Year:

2019

Language:

english

File:

PDF, 2.50 MB

english, 2019

44

Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS)

Playdon, Mary C., Joshi, Amit D., Tabung, Fred K., Cheng, Susan, Henglin, Mir, Kim, Andy, Lin, Tengda, van Roekel, Eline H., Huang, Jiaqi, Krumsiek, Jan, Wang, Ying, Mathé, Ewy, Temprosa, Marinella, M

Journal:

Year:

2019

File:

PDF, 2.50 MB

2019

45

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics

Mathé, Ewy, Zhang, Chi, Wang, Kai, Ning, Xia, Guo, Yan, Zhao, Zhongming

Journal:

Year:

2019

Language:

english

File:

PDF, 449 KB

english, 2019

46

The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases

Zhao, Zhongming, Dai, Yulin, Zhang, Chi, Mathé, Ewy, Wei, Lai, Wang, Kai

Journal:

BMC Bioinformatics

Year:

2019

Language:

english

File:

PDF, 430 KB

english, 2019

47

Biomarkers of Exposure and Effect in the Lungs of Smokers, Non-Smokers and Electronic Cigarette Users

Song, Min-Ae, Freudenheim, Jo L., Brasky, Theodore M., Mathé, Ewy A., McElroy, Joseph P, Nickerson, Quentin A, Reisinger, Sarah A., Smiraglia, Dominic J., Weng, Daniel Y, Ying, Kevin L, Wewers, Mark D

Journal:

Cancer Epidemiology Biomarkers & Prevention

Year:

2019

File:

PDF, 6.33 MB

2019

48

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics

Mathé, Ewy, Zhang, Chi, Wang, Kai, Ning, Xia, Guo, Yan, Zhao, Zhongming

Journal:

Year:

2019

File:

PDF, 449 KB

2019

49

The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases

Zhao, Zhongming, Dai, Yulin, Zhang, Chi, Mathé, Ewy, Wei, Lai, Wang, Kai

Journal:

BMC Bioinformatics

Year:

2019

File:

PDF, 430 KB

2019

50

Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge

Eicher, Tara, Patt, Andrew, Kautto, Esko, Machiraju, Raghu, Mathé, Ewy, Zhang, Yan

Journal:

BMC Bioinformatics

Year:

2019

File:

PDF, 1.54 MB

2019