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1

Data Analysis Strategies in Medical Imaging

Parmar, Chintan, Barry, Joseph D., Hosny, Ahmed, Quackenbush, John, Aerts, Hugo JWL

Journal:

Clinical Cancer Research

Year:

2018

Language:

english

File:

PDF, 498 KB

english, 2018

2

Artificial intelligence in radiology

Hosny, Ahmed, Parmar, Chintan, Quackenbush, John, Schwartz, Lawrence H., Aerts, Hugo J. W. L.

Journal:

Nature Reviews Cancer

Year:

2018

Language:

english

File:

PDF, 945 KB

english, 2018

3

Longitudinal study of the impacts of land cover change on hydrologic response in four mesoscale watersheds in New York State, USA

Shaw, Stephen B., Marrs, John, Bhattarai, Nishan, Quackenbush, Lindi

Journal:

Journal of Hydrology

Year:

2014

Language:

english

File:

PDF, 2.27 MB

english, 2014

4

Inconsistency in large pharmacogenomic studies

Haibe-Kains, Benjamin, El-Hachem, Nehme, Birkbak, Nicolai Juul, Jin, Andrew C., Beck, Andrew H., Aerts, Hugo J. W. L., Quackenbush, John

Journal:

Year:

2013

Language:

english

File:

PDF, 2.02 MB

english, 2013

5

Measurement of electro-optic properties of ferroelectric thin films using the ultimate ellipsometer

Teowee, G., Baertlein, C. D., Simpson, John T., Zhao, Tianji, Mansuripur, M., Quackenbush, E. L., Boulton, J. M., Uhlmann, D. R.

Journal:

Integrated Ferroelectrics

Year:

1995

Language:

english

File:

PDF, 567 KB

english, 1995

6

Swimbladder Leiomyosarcoma in Atlantic Salmon (Salmo salar) in North America

Bowser, Paul R., Casey, James W., Casey, Rufina N., Quackenbush, Sandra L., Lofton, Larry, Coll, John A., Cipriano, Rocco C.

Journal:

Journal of Wildlife Diseases

Year:

2012

Language:

english

File:

PDF, 1.25 MB

english, 2012

7

Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology

Wu, Weimiao, Parmar, Chintan, Grossmann, Patrick, Quackenbush, John, Lambin, Philippe, Bussink, Johan, Mak, Raymond, Aerts, Hugo J. W. L.

Journal:

Frontiers in Oncology

Year:

2016

Language:

english

File:

PDF, 8.54 MB

english, 2016

8

High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report

Hersh, Craig P., Adcock, Ian M., Celedón, Juan C., Cho, Michael H., Christiani, David C., Himes, Blanca E., Kaminski, Naftali, Mathias, Rasika A., Meyers, Deborah A., Quackenbush, John, Redline, Susan

Journal:

Annals of the American Thoracic Society

Year:

2019

Language:

english

File:

PDF, 663 KB

english, 2019

9

Observations of Landslides Caused by the April 2015 Gorkha, Nepal, Earthquake Based on Land, UAV, and Satellite Reconnaissance

Zekkos, Dimitrios, Clark, Marin, Whitworth, Michael, Greenwood, William, West, A. Joshua, Roback, Kevin, Li, Gen, Chamlagain, Deepak, Manousakis, John, Quackenbush, Paul, Medwedeff, William, Lynch, Je

Journal:

Earthquake Spectra

Year:

2017

File:

PDF, 1.94 MB

2017

10

The quest for the mechanisms of life

Maria I. Klapa, John Quackenbush

Journal:

Biotechnology and Bioengineering

Year:

2003

Language:

english

File:

PDF, 63 KB

english, 2003

11

Time-series integrated “omic” analyses to elucidate short-term stress-induced responses in plant liquid cultures

Bhaskar Dutta, Harin Kanani, John Quackenbush, Maria I. Klapa

Journal:

Biotechnology and Bioengineering

Year:

2009

Language:

english

File:

PDF, 1.24 MB

english, 2009

12

High-throughput amplicon scanning of the TP53 gene in breast cancer using high-resolution fluorescent melting curve analyses and automatic mutation calling

Roy Bastien, Tracey B. Lewis, Jason E. Hawkes, John F. Quackenbush, Thomas C. Robbins, Juan Palazzo, Charles M. Perou, Philip S. Bernard

Journal:

Year:

2008

Language:

english

File:

PDF, 367 KB

english, 2008

13

Technical improvement in permanent seed implantation: a two-stage brachytherapy system. Description and comparison with current technique

Peter D Grimm, John C Blasko, John E Sylvester, Charles Heaney, James Gasparich, Jeffrey Quackenbush, Jim Gottesman, Jim Downey, Doug Grier, Tim Roddy, Roger Nellans, Narender Sood, David Wahl

Journal:

Year:

2004

Language:

english

File:

PDF, 351 KB

english, 2004

14

GCOD - GeneChip Oncology Database

Fenglong Liu, Joseph A White, Corina Antonescu, Daniel Gusenleitner, John Quackenbush

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.39 MB

english, 2011

15

The limits of log-ratios

Vasily Sharov, Ka Yin Kwong, Bryan Frank, Emily Chen, Jeremy Hasseman, Renee Gaspard, Yan Yu, Ivana Yang, John Quackenbush

Journal:

BMC Biotechnology

Year:

2004

Language:

english

File:

PDF, 3.42 MB

english, 2004

16

Genetic basis of murine antibacterial defense to streptococcal lung infection

John W. Hollingsworth, Gregory Whitehead, Katherine Gray Berman, Erin McElvania Tekippe, M. Ian Gilmour, Jennie E. Larkin, John Quackenbush, David A. Schwartz

Journal:

Year:

2007

Language:

english

File:

PDF, 413 KB

english, 2007

17

Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly

Scott C. Fahrenkrug, Timothy P.L. Smith, Brad A. Freking, Jennifer Cho, Joseph White, Jeff Vallet, Tommy Wise, Gary Rohrer, Geo Pertea, Razvan Sultana, John Quackenbush, John W. Keele

Journal:

Mammalian Genome

Year:

2002

Language:

english

File:

PDF, 97 KB

english, 2002

18

Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index

TadS. Sonstegard, Anthony V. Capuco, Joseph White, Curtis P. Van Tassell, Erin E. Connor, Jennifer Cho, Razvan Sultana, Larry Shade, James E. Wray, Kevin D. Wells, John Quackenbush

Journal:

Mammalian Genome

Year:

2002

Language:

english

File:

PDF, 181 KB

english, 2002

19

Training school psychologists in neuropsychological assessment: Current practices and trends

George W. Hynd, Ray Quackenbush, John E. Obrzut

Journal:

Journal of School Psychology

Year:

1980

Language:

english

File:

PDF, 327 KB

english, 1980

20

Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome

H. Stanley Kim, Yan Yu, Erik C. Snesrud, Linda P. Moy, Lara D. Linford, Brian J. Haas, William C. Nierman, John Quackenbush

Journal:

The Plant Journal

Year:

2005

Language:

english

File:

PDF, 472 KB

english, 2005

21

The Environmental Health Engagement Profile: What People Think and Do About Environmental Health

Jane K. Dixon, Karrie C. Hendrickson, Elizabeth Ercolano, Robi Quackenbush, John P. Dixon

Journal:

Public Health Nursing

Year:

2009

Language:

english

File:

PDF, 169 KB

english, 2009

22

Identification of genes involved in colon cancer metastasis using cDNA microarrays

Hegde, Priti, Earle-Hughes, Julie, Abernathy, Kristie, Gay, Cheryl, Dharap, Sonia, Saeed, Alexander I., Sharov, #1Vasily, Lee, Norman H., Yeatman, Timothy, Quackenbush, John

Journal:

Nature Genetics

Year:

1999

Language:

english

File:

PDF, 113 KB

english, 1999

23

Use of the Rat Gene Index to examine gene expression patterns from Src-transformed rat fibroblasts that exhibit broad differences in metastatic potential

Malek, Renae L., Guo, Qingbin, Ruffy, Mauro, Liu, Edison T., Holt, Ingeborg, Chandra, Ishwar, Liang, Feng, Upton, Jonathan, Quackenbush, John, Jove, Richard, Yeatman, Timothy J., Lee, Norman H.

Journal:

Nature Genetics

Year:

1999

Language:

english

File:

PDF, 91 KB

english, 1999

24

COMPUTATIONAL GENETICS: COMPUTATIONAL ANALYSIS OF MICROARRAY DATA

Quackenbush, John

Journal:

Nature Reviews Genetics

Year:

2001

Language:

english

File:

PDF, 1.15 MB

english, 2001

25

Top-down standards will not serve systems biology

Quackenbush, John, Stoeckert, Christian, Ball, Catherine, Brazma, Alvis, Gentleman, Robert, Huber, Wolfgang, Irizarry, Rafael, Salit, Marc, Sherlock, Gavin, Spellman, Paul

Journal:

Year:

2006

Language:

english

File:

PDF, 120 KB

english, 2006

26

10.1038/76128

Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Karamycheva, Svetlana, Salzberg, Steven L.

Journal:

Nature Genetics

Year:

2000

File:

PDF, 80 KB

2000

27

10.1038/76133

Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Karamycheva, Svetlana, Salzberg, Steven L.

Journal:

Nature Medicine

Year:

2000

Language:

english

File:

PDF, 78 KB

english, 2000

28

10.1038/76126

Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Karamycheva, Svetlana, Salzberg, Steven L.

Journal:

Nature Genetics

Year:

2000

Language:

english

File:

PDF, 100 KB

english, 2000

29

10.1038/81525

Quackenbush, John

Journal:

Nature Genetics

Year:

2000

Language:

english

File:

PDF, 265 KB

english, 2000

30

Data standards for 'omic' science

Quackenbush, John

Journal:

Nature Biotechnology

Year:

2004

Language:

english

File:

PDF, 82 KB

english, 2004

31

What would you do if you could sequence everything?

Kahvejian, Avak, Quackenbush, John, Thompson, John F

Journal:

Nature Biotechnology

Year:

2008

Language:

english

File:

PDF, 908 KB

english, 2008

32

ESR1 gene amplification in breast cancer: a common phenomenon?

Brown, Lindsay A, Hoog, Jeremy, Chin, Suet-Feung, Tao, Yu, Zayed, Abd Alnaser, Chin, Koei, Teschendorff, Andrew E, Quackenbush, John F, Marioni, John C, Leung, Samuel

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 137 KB

english, 2008

33

10.1038/ng0901-4

Quackenbush, John

Journal:

Nature Genetics

Year:

2001

Language:

english

File:

PDF, 697 KB

english, 2001

34

Microarray data normalization and transformation

Quackenbush, John

Journal:

Nature Genetics

Year:

2002

Language:

english

File:

PDF, 2.28 MB

english, 2002

35

10.1038/ng1201-365

Brazma, Alvis, Hingamp, Pascal, Quackenbush, John, Sherlock, Gavin, Spellman, Paul, Stoeckert, Chris, Aach, John, Ansorge, Wilhelm, Ball, Catherine A., Causton, Helen C., Gaasterland, Terry, Glenisson

Journal:

Nature Genetics

Year:

2001

Language:

english

File:

PDF, 527 KB

english, 2001

36

Independence and reproducibility across microarray platforms

Larkin, Jennie E, Frank, Bryan C, Gavras, Haralambos, Sultana, Razvan, Quackenbush, John

Journal:

Year:

2005

Language:

english

File:

PDF, 364 KB

english, 2005

37

Identification of Src transformation fingerprint in human colon cancer

Malek, Renae L, Irby, Rosalyn B, Guo, Qingbin M, Lee, Kerry, Wong, Sylvia, He, Mei, Tsai, Jennifer, Frank, Bryan, Liu, Edison T, Quackenbush, John

Journal:

Year:

2002

Language:

english

File:

PDF, 308 KB

english, 2002

38

The identification of creativity in adolescents.

Piers, Ellen V., Daniels, Jacqueline M., Quackenbush, John F.

Journal:

Journal of Educational Psychology

Year:

1960

Language:

english

File:

PDF, 381 KB

english, 1960

39

Arylsulfonate esters of fatty alcohols as hypocholesterolemic agents. I: Oleyl and linoleyl p-toluenesulfonates

Forrest W. Quackenbush, Phillip G. Rand, John E. MacNintch

Journal:

Year:

1977

Language:

english

File:

PDF, 184 KB

english, 1977

40

New books

K. V. Kordesch, John Pinzelik, J. H. Jones, F. W. Quackenbush, J. R. Anfinsen

Journal:

Journal of the American Oil Chemists' Society

Year:

1968

Language:

english

File:

PDF, 1.21 MB

english, 1968

41

Twisted world-sheet gauge fields and string models

John Quackenbush

Journal:

Physics Letters B

Year:

1990

Language:

english

File:

PDF, 349 KB

english, 1990

42

Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages

Liwang Cui, Qi Fan, Yi Hu, Svetlana A. Karamycheva, John Quackenbush, Benjawan Khuntirat, Jetsumon Sattabongkot, Jane M. Carlton

Journal:

Molecular and Biochemical Parasitology

Year:

2005

Language:

english

File:

PDF, 195 KB

english, 2005

43

Extracting meaning from functional genomics experiments

John Quackenbush

Journal:

Toxicology and Applied Pharmacology

Year:

2005

Language:

english

File:

PDF, 95 KB

english, 2005

44

Response to Shields: ‘MIAME, we have a problem’

John Quackenbush, Rafael A. Irizarry

Journal:

Trends in Genetics

Year:

2006

Language:

english

File:

PDF, 78 KB

english, 2006

45

HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition

Karin Hellner, Jessica Mar, Frank Fang, John Quackenbush, Karl Münger

Journal:

Year:

2009

Language:

english

File:

PDF, 531 KB

english, 2009

46

The African trypanosome genome

Najib M El-Sayed, Priti Hegde, John Quackenbush, Sara E Melville, John E Donelson

Journal:

International Journal for Parasitology

Year:

2000

Language:

english

File:

PDF, 802 KB

english, 2000

47

AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum

Vishvanath Nene, Dan Lee, John Quackenbush, Robert Skilton, Stephen Mwaura, Malcolm J. Gardner, Richard Bishop

Journal:

International Journal for Parasitology

Year:

2002

Language:

english

File:

PDF, 254 KB

english, 2002

48

Data-driven normalization strategies for high-throughput quantitative RT-PCR

Jessica C Mar, Yasumasa Kimura, Kate Schroder, Katharine M Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume, John Quackenbush

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 636 KB

english, 2009

49

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)

Martin J Aryee, José A Gutiérrez-Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 376 KB

english, 2009

50

Multiple-input multiple-output causal strategies for gene selection

Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos Sotiriou, John Quackenbush

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 465 KB

english, 2011

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