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1

A travel guide to Cytoscape plugins

Saito, Rintaro, Smoot, Michael E, Ono, Keiichiro, Ruscheinski, Johannes, Wang, Peng-Liang, Lotia, Samad, Pico, Alexander R, Bader, Gary D, Ideker, Trey

Journal:

Year:

2012

Language:

english

File:

PDF, 812 KB

english, 2012

2

Correlation of the complete version of the Selvester QRS scoring system with quantitative anatomic findings for multiple left ventricular myocardial infarcts

Dorina C. Sevilla, Nancy B. Wagner, Robert Pegues, Steven L. Peck, Eileen M. Mikat, Raymond E. Ideker, Grover Hutchins, Keith A. Reimer, Donald B. Hackel, Ronald H. Selvester, Galen S. Wagner

Journal:

The American Journal of Cardiology

Year:

1992

Language:

english

File:

PDF, 484 KB

english, 1992

3

Advances in alternative cementitious binders

M.C.G. Juenger, F. Winnefeld, J.L. Provis, J.H. Ideker

Journal:

Cement and Concrete Research

Year:

2011

Language:

english

File:

PDF, 1.09 MB

english, 2011

4

Digital Twin of Experimental Smart Manufacturing Assembly System for Industry 4.0 Concept

Å½idek, Kamil, PiteÄ¾, JÃ¡n, AdÃ¡mek, Milan, LazorÃk, Peter, HoÅ¡ovskÃ½, Alexander

Journal:

Year:

2020

File:

PDF, 10.36 MB

2020

5

A Decade of Systems Biology

Chuang, Han-Yu, Hofree, Matan, Ideker, Trey

Journal:

Annual Review of Cell and Developmental Biology

Year:

2010

Language:

english

File:

PDF, 2.59 MB

english, 2010

6

Alkali–silica reaction: Current understanding of the reaction mechanisms and the knowledge gaps

Rajabipour, Farshad, Giannini, Eric, Dunant, Cyrille, Ideker, Jason H., Thomas, Michael D.A.

Journal:

Cement and Concrete Research

Year:

2015

Language:

english

File:

PDF, 1.36 MB

english, 2015

7

Influence of aggregate type on conversion and strength in calcium aluminate cement concrete

Adams, Matthew P., Ideker, Jason H.

Journal:

Cement and Concrete Research

Year:

2017

Language:

english

File:

PDF, 2.72 MB

english, 2017

8

Using deep learning to model the hierarchical structure and function of a cell

Ma, Jianzhu, Yu, Michael Ku, Fong, Samson, Ono, Keiichiro, Sage, Eric, Demchak, Barry, Sharan, Roded, Ideker, Trey

Journal:

Year:

2018

Language:

english

File:

PDF, 2.00 MB

english, 2018

9

pyNBS: A Python implementation for network-based stratification of tumor mutations

Huang, Justin K, Jia, Tongqiu, Carlin, Daniel E, Ideker, Trey

Journal:

Year:

2018

Language:

english

File:

PDF, 243 KB

english, 2018

10

Identifying Epistasis in Cancer Genomes: A Delicate Affair

van de Haar, Joris, Canisius, Sander, Yu, Michael K., Voest, Emile E., Wessels, Lodewyk F.A., Ideker, Trey

Journal:

Year:

2019

Language:

english

File:

PDF, 4.02 MB

english, 2019

11

Test methods for evaluating preventive measures for controlling expansion due to alkali–silica reaction in concrete

Michael Thomas, Benoit Fournier, Kevin Folliard, Jason Ideker, Medhat Shehata

Journal:

Cement and Concrete Research

Year:

2006

Language:

english

File:

PDF, 674 KB

english, 2006

12

Usefulness of Aggressive Behaviour Risk Assessment Tool for prospectively identifying violent patients in medical and surgical units

Son Chae Kim, Kristyn Ideker, Dale Todicheeney-Mannes

Journal:

Journal of Advanced Nursing

Year:

2012

Language:

english

File:

PDF, 130 KB

english, 2012

13

An Up-Down Bayesian, Defibrillation Efficacy Estimator

ALIKI T. COMPOS, ROBERT A. MALKIN, RAYMOND E. IDEKER

Journal:

Pacing and Clinical Electrophysiology

Year:

1997

Language:

english

File:

PDF, 3.68 MB

english, 1997

14

The Effect of Cardiac Compression on Defibrillation Efficacy and the Upper Limit of Vulnerability

SALIM F. IDRISS, MARK P. ANSTADT, GEORGE L. ANSTADT, RAYMOND E. IDEKER

Journal:

Journal of Cardiovascular Electrophysiology

Year:

1995

Language:

english

File:

PDF, 4.59 MB

english, 1995

15

The Ventricular Defibrillation and Upper Limit of Vulnerability Dose-Response Curves

ROBERT A. MALKIN, JOSEPH J. SOUZA, RAYMOND E. IDEKER

Journal:

Journal of Cardiovascular Electrophysiology

Year:

1997

Language:

english

File:

PDF, 3.57 MB

english, 1997

16

Review of Mechanisms by Which Electrical Stimulation Alters the Transmembrane Potential

JONATHAN C. NEWTON, STEPHEN B. KNISLEY, XIAOHONG ZHOU, ANDREW E. POLLARD, RAYMOND E. IDEKER

Journal:

Journal of Cardiovascular Electrophysiology

Year:

1999

Language:

english

File:

PDF, 4.60 MB

english, 1999

17

Modeling cellular machinery through biological network comparison

Sharan, Roded, Ideker, Trey

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 531 KB

english, 2006

18

Cytoscape 2.8: new features for data integration and network visualization

Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L., Ideker, T.

Journal:

Year:

2011

Language:

english

File:

PDF, 160 KB

english, 2011

19

Evaluation of a QRS scoring system for estimating myocardial infarct size. VI: Identification of screening criteria for non-acute myocardial infarcts

William D. Anderson, Nancy B. Wagner, Kerry L. Lee, Richard D. White, James Yuschak, Victor S. Behar, Ronald H. Selvester, Raymond E. Ideker, Galen S. Wagner

Journal:

The American Journal of Cardiology

Year:

1988

Language:

english

File:

PDF, 512 KB

english, 1988

20

Effect of environmental conditions on expansion in concrete due to alkali–silica reaction (ASR)

Benoit Fournier, Jason H. Ideker, Kevin J. Folliard, Michael D.A. Thomas, Pierre-Claver Nkinamubanzi, Ray Chevrier

Journal:

Materials Characterization

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

21

Estimation of conduction velocity vector fields from epicardial mapping data

Bayly, P.V., KenKnight, B.H., Rogers, J.M., Hillsley, R.E., Ideker, R.E., Smith, W.M.

Journal:

IEEE Transactions on Biomedical Engineering

Year:

1998

Language:

english

File:

PDF, 258 KB

english, 1998

22

Eccentric Dipole in a Spherical Medium: Generalized Expression for Surface Potentials

Brody, Daniel A., Terry, Fred H., Ideker, Raymond E.

Journal:

IEEE Transactions on Biomedical Engineering

Year:

1973

Language:

english

File:

PDF, 776 KB

english, 1973

23

A gene ontology inferred from molecular networks

Dutkowski, Janusz, Kramer, Michael, Surma, Michal A, Balakrishnan, Rama, Cherry, J Michael, Krogan, Nevan J, Ideker, Trey

Journal:

Nature Biotechnology

Year:

2012

Language:

english

File:

PDF, 2.38 MB

english, 2012

24

The correlation of the defibrillation threshhold and the upper limit of vulnerability using catheter-patch defibrillating electrodes

Katherine M Kavanagh, Jenny H Harrison, Ellen G Dixon, William M Smith, J.Marcus Wharton, Raymond E Ideker

Journal:

Journal of the American College of Cardiology

Year:

1990

File:

PDF, 335 KB

1990

25

944-117The Effect of Pacing Site on the Upper Limit of Ventricular Vulnerability

Salim F. Idriss, Letealia M. Oliver, Patrick D. Wolf, Raymond E. Ideker

Journal:

Journal of the American College of Cardiology

Year:

1995

Language:

english

File:

PDF, 289 KB

english, 1995

26

Integrative approaches for finding modular structure in biological networks

Mitra, Koyel, Carvunis, Anne-Ruxandra, Ramesh, Sanath Kumar, Ideker, Trey

Journal:

Nature Reviews Genetics

Year:

2013

Language:

english

File:

PDF, 2.64 MB

english, 2013

27

For the record

Zhou, Xiaohong, Smith, William M., Johnson, Chad, Ideker, Raymond E.

Journal:

Year:

2007

Language:

english

File:

PDF, 118 KB

english, 2007

28

Quantification of activation patterns during ventricular fibrillation in open-chest porcine left ventricle and septum

Huang, Jian, Walcott, Greg P., Killingsworth, Cheryl R., Melnick, Sharon B., Rogers, Jack M., Ideker, Raymond E.

Journal:

Year:

2005

Language:

english

File:

PDF, 615 KB

english, 2005

29

Siri of the Cell: What Biology Could Learn from the iPhone

Carvunis, Anne-Ruxandra, Ideker, Trey

Journal:

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

30

Physical Network Models

Yeang, Chen-Hsiang, Ideker, Trey, Jaakkola, Tommi

Journal:

Journal of Computational Biology

Year:

2004

Language:

english

File:

PDF, 507 KB

english, 2004

31

Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data

Ideker, Trey, Thorsson, Vesteinn, Siegel, Andrew F., Hood, Leroy E.

Journal:

Journal of Computational Biology

Year:

2000

Language:

english

File:

PDF, 449 KB

english, 2000

32

Comparison of the defibrillation threshold and the upper limit of ventricular vulnerability

Chen, P. S., Shibata, N., Dixon, E. G., Martin, R. O., Ideker, R. E.

Journal:

Year:

1986

Language:

english

File:

PDF, 1.44 MB

english, 1986

33

Pacing After Shocks Stronger Than the Upper Limit of Vulnerability : Impact on Fibrillation Induction

Chattipakorn, N., Fotuhi, P. C., Sreenan, C. M., White, J. B., Ideker, R. E.

Journal:

Year:

2000

Language:

english

File:

PDF, 699 KB

english, 2000

34

Detection and localization of multiple epicardial electrical generators by a two-dipole ranging technique

Mirvis, D. M., Keller, F. W., Ideker, R. E., Cox, J. W., Dowdie, R. F., Zettergren, D. G.

Journal:

Circulation Research

Year:

1977

Language:

english

File:

PDF, 2.82 MB

english, 1977

35

Relative dipolar behavior of the equivalent T wave generator: quantitative comparison with ventricular excitation in the rabbit heart

Brody, D. A., Mirvis, D. M., Ideker, R. E., Cox, J. W., Keller, F. W., Larsen, R. A., Bandura, J. P.

Journal:

Circulation Research

Year:

1977

Language:

english

File:

PDF, 744 KB

english, 1977

36

Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

Jaeger, Philipp A., McElfresh, Cameron, Wong, Lily R., Ideker, Trey, Liu, S.-J.

Journal:

Applied and Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 1.41 MB

english, 2015

37

Interpreting Metabolomic Profiles using Unbiased Pathway Models

Deo, Rahul C., Hunter, Luke, Lewis, Gregory D., Pare, Guillaume, Vasan, Ramachandran S., Chasman, Daniel, Wang, Thomas J., Gerszten, Robert E., Roth, Frederick P., Ideker, Trey

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

38

Bioinformatics in the human interactome project

Ideker, T., Valencia, A.

Journal:

Year:

2006

Language:

english

File:

PDF, 39 KB

english, 2006

39

The Use of Consciousness-Raising Techniques in Teaching the Verb ‘be’ to Students of Vocational Colleges

Idek, Sirhajwan, Fong, Lee Lai

Journal:

Procedia - Social and Behavioral Sciences

Year:

2015

Language:

english

File:

PDF, 350 KB

english, 2015

40

ICAAR 1974–2016 conferences for examination of AAR in concrete

Andiç-Çakır, Özge, Poole, Alan B., Ideker, Jason H.

Journal:

Proceedings of the ICE - Construction Materials

Year:

2016

Language:

english

File:

PDF, 1.09 MB

english, 2016

41

Network propagation: a universal amplifier of genetic associations

Cowen, Lenore, Ideker, Trey, Raphael, Benjamin J., Sharan, Roded

Journal:

Nature Reviews Genetics

Year:

2017

Language:

english

File:

PDF, 593 KB

english, 2017

42

A mechanistic study on mitigation of alkali-silica reaction by fine lightweight aggregates

Li, Chang, Thomas, Michael D.A., Ideker, Jason H.

Journal:

Cement and Concrete Research

Year:

2017

Language:

english

File:

PDF, 2.11 MB

english, 2017

43

Visible Machine Learning for Biomedicine

Yu, Michael K., Ma, Jianzhu, Fisher, Jasmin, Kreisberg, Jason F., Raphael, Benjamin J., Ideker, Trey

Journal:

Year:

2018

Language:

english

File:

PDF, 746 KB

english, 2018

44

Use of iodine for improving phase quantification using x-ray tomography

Deboodt, Tyler, Wildenschild, Dorthe, Ideker, Jason H., Isgor, O. Burkan

Journal:

Cement and Concrete Research

Year:

2019

Language:

english

File:

PDF, 1.87 MB

english, 2019

45

The Use of Consciousness-Raising Tasks in Learning and Teaching of Subject-Verb Agreement

Idek, Sirhajwan, Lai Fong, Lee, Kaur Sidhu, Gurnam

Journal:

English Language Teaching

Year:

2013

File:

PDF, 159 KB

2013

46

Using Supplementary Cementitious Materials to Mitigate Alkali-Silica Reaction in Concrete with Recycled-Concrete Aggregate

Adams, Matthew P., Ideker, Jason H.

Journal:

Journal of Materials in Civil Engineering

Year:

2020

File:

PDF, 560 KB

2020

47

Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response

Silva, Erica, Michaca, Manuel, Munson, Brenton, Bean, Gordon J., Jaeger, Philipp A., Licon, Katherine, Winzeler, Elizabeth A., Ideker, Trey

Journal:

G3 Genes|Genome|Genetics

Year:

2020

File:

PDF, 3.92 MB

2020

48

Right-sided vagus nerve stimulation inhibits induced spinal cord seizures

R. Shane Tubbs, E. George Salter, Cheryl Killingsworth, Dennis L. Rollins, William M. Smith, Raymond E. Ideker, John C. Wellons III, Jeffrey P. Blount, W. Jerry Oakes

Journal:

Clinical Anatomy

Year:

2007

Language:

english

File:

PDF, 75 KB

english, 2007

49

Aneurysm of a saphenous vein bypass graft associated with aneurysms of native coronary arteries

Dean A. Bramlet, Dr. Victor S. Behar, Raymond E. Ideker

Journal:

Catheterization and Cardiovascular Interventions

Year:

1982

Language:

english

File:

PDF, 794 KB

english, 1982

50

An Automated Technique for Identification and Analysis of Activation Fronts in a Two-Dimensional Electrogram Array

Kurt D. Bollacker, Edward V. Simpson, Russel E. Hillsley, Susan M. Blanchard, Ronald J. Gerstle, Gregory P. Walcott, Richard L. Callihan, Michael C. King, William M. Smith, Raymond E. Ideker

Journal:

Computers and Biomedical Research

Year:

1994

File:

PDF, 529 KB

1994

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